Abiotic Stress Tolerance in Plants: Toward the Improvement of Global Environment and Food - PDF Free Download (2024)


Abiotic Stress Tolerance in Plants Toward the Improvement of Global Environment and Food Edited by

ASHWANI K. RAI Banaras Hindu University, Varanasi, India and

TERUHIRO TAKABE Meijo University, Nagoya, Japan

A C.I.P. Catalogue record for this book is available from the Library of Congress.


1-4020-4388-0 (HB) 978-1-4020-4388-8 (HB) 1-4020-4389-9 (e-book) 978-1-4020-4389-5 (e-book)

Published by Springer, P.O. Box 17, 3300 AA Dordrecht, The Netherlands. www.springer.com

Cover illustration by Dr. Hiroyasu Ebinuma, Tokyo, Japan Printed on acid-free paper

All Rights Reserved © 2006 Springer No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed in the Netherlands.

Contents Section I: Signal transduction 1. Stress signal transduction: components, pathways and network integration

1 3


2. Identification of salt-responsive genes in monocotyledonous plants: from transcriptome to functional analysis AKIHIRO UEDA, SHIRO MITSUYA AND TETSUKO TAKABE 3. Phosphorylation of RNA polymerase II C-terminal domain and plant osmotic-stress responses




Section II: Temperature stress 4. Trienoic fatty acids and temperature tolerance of higher plants

59 61


Section III: Oxidative stresses 5. Nitric oxide research in agriculture: bridging the plant and bacterial realms MICHAEL F . COHEN, MARK MAZZOLA AND HIDEO

69 71


6. Ultraviolet radiation stress: molecular and physiological adaptations in trees S. S. SINGH, PANKAJ KUMAR AND ASHWANI K. RAI 7. Involvement of aldehyde dehydrogenase in alleviation of post-anoxic injury in rice NAOKI MEGURO, HIROYUKI TSUJI, NOBUHIRO TSUTSUMI, MIKIO NAKAZONO AND ATSUSHI HIRAI





Section IV: Phytoremediation 8. Genetic engineering stress tolerant plants for phytoremediation DANIKA L. LEDUC AND NORMAN TERRY

121 123

Section V: Osmotic stresses 9. Metabolic engineering of glycinebetaine TERUHIRO TAKABE, VANDNA RAI AND TAKASHI HIBINO 10. Induction of biosynthesis of osmoprotectants in higher plants by hydrogen peroxide and its application to agriculture AKIO UCHIDA, TOMOKO TAKABE, TETSUKO TAKABE AND ANDRE T. JAGENDORF Section VI: Ion homeostasis 11. Na+/H+ antiporters in plants and cyanobacteria RUNGAROON WADITEE, YOsh*tO TANAKA

135 137


161 163 AND


12. Structural and functional relationship between cation transporters and channels



Section VII: Nutrition 13. Is cellulose synthesis enhanced by expression of sucrose synthase in poplar? TAKAHISA HAYASHI, TERUKO KONISHI, YASUNORI

185 187


14. Nitrogen metabolism in cyanobacteria under osmotic stress



Section VIII: Structural responses 15. Ultrastructural effects of salinity stress in higher plants HIROSHI MIYAKE, SHIRO MITSUYA AND MD. SHAHIDUR RAHMAN

213 215



Section IX: Development of Biotechnology 16. Genetic diversity of saline coastal rice (Oryza Sativa L.) landraces of Bangladesh ZEBA I. SERAJ, LAISA A. LISA, M. RAFIQUL ISLAM, ROKEYA BEGUM AND DEEPOK K. DAS 17. Development of marker-free vectors, and its application


227 229

gene-exchange 245


18. Toward the development of biotechnology in Asia TETSUO MATSUMOTO AND RITA P. LAUDE




Preface Stresses in plants caused by salt, drought, temperature, oxygen, and toxic compounds are the principal reason for reduction in crop yield. For example, high salinity in soils accounts for large decline in the yield of a wide variety of crops world over; ~1000 million ha of land is affected by soil salinity. Increased sunlight leads to the generation of reactive oxygen species, which damage the plant cells. The threat of global environment change makes it increasingly demanding to generate crop plants that could withstand such harsh conditions. Much progress has been made in the identification and characterization of the mechanisms that allow plants to tolerate abiotic stresses. The understanding of metabolic fluxes and the main constraints responsible for the production of compatible solutes and the identification of many transporters, collectively open the possibility of genetic engineering in crop plants with the concomitant improved stress tolerance. Abiotic Stress Tolerance in Plants is a new book with focus on how plants adapt to abiotic stress and how genetic engineering could improve the global environment and food supply. Especially, the application of biotechnology in Asia and Africa would be important. Environmental stress impact is not only on current crop species, but is also the paramount barrier to the introduction of crop plants into areas not currently being used for agriculture. Stresses are likely to enhance the severity of problems to be faced by plants in the near future. The present book brings together contributions from many laboratories around the world in order to discuss and compare the current knowledge about the role of stress genes in plant stress tolerance. In addition, strategies to introduce these genes into economically important crops and its effects on plant productivity are discussed. We express our thanks to all the contributors. Our sincere thanks are especially due to Prof. Tetsuko Takabe for her kind help in going through the contents and its arrangement. Finally, it is a profound pleasure to thank Springer for taking up the publication of this book. July, 2005 Ashwani K Rai Teruhiro Takabe



1. STRESS SIGNAL TRANSDUCTION: components, pathways and network integration


Donald Danforth Plant Science Center, 975. N. Warson Road, St. Louis, Missouri 63132, USA 2 International Center for Tropical Agriculture (CIAT), A.A, 6713, Cali, COLOMBIA 3 Correspondence author e-mail: [emailprotected]

Abstract. Drought, high soil salinity, and low temperature are common adverse environmental conditions that limit crop productivity worldwide. Plants respond to these abiotic stresses partly by activating the expression of stress-responsive genes. The products of some of these genes can increase plant tolerance to the stresses. Understanding how stress-responsive genes are activated by abiotic stress will help us to breed or engineer stress tolerant crop plants. Genetic and other studies are revealing components that are involved in the signal transduction forabiotic stresses. The pathways that lead to the activation of stress-responsive genes and the network that integrates these pathways are being discovered in model plant systems. This chapter discusses some recent progresses in the elucidation of abiotic stress signaling mechanisms.

1. INTRODUCTION Adverse environmental conditions such as drought, high soil salinity, and temperature extremes are found in many agricultural areas. These abiotic stresses can result in severe yield loss to agricultural crops. Plants exhibit various responses to these stresses at the molecular, cellular, and whole plant levels [1-4]. These responses may contribute to increased tolerance to the stresses [5-8]. To breed or genetically engineer plant stress tolerance, it is imperative to identify the genes that control these traits and to understand how these genes and their products are regulated. With the availability of complete information on a couple of plant genomes and of various genomics and proteomics tools, knowledge on plant abiotic stress responses has been advanced at a great pace in the last few years. In particular, documentation of genes that are regulated by stresses is comprehensive for the model plant Arabidopsis and should be complete for rice soon as well. Nonetheless, abiotic stress signaling mechanisms have been proven to be very complex, and there is still much more to learn. To date, only a handful of genes that play critical roles in plant adaptation to stresses have been identified with confidence. Few pathways that mediate stress responses are revealed in complete. In this chapter, we will give an 3 Ashwani K. Rai and Teruhiro Takabe (eds.), Abiotic Stress Tolerance in Plants, 3-29. © 2006 Springer. Printed in the Netherlands.



overview of the current knowledge on signal transduction mechanisms responsible for signal perception, amplification, transmission, and final activation of stress responses. We will discuss examples of genetic studies or other studies where there is some supporting genetic evidence. This overview will mainly focus on advances made during the past two years since our last review on abiotic stress signal transduction was published [9]. 2. ABIOTIC STRESS-REGULATED GENES One major response of plants upon encountering abiotic stresses is the activation of stress-responsive genes. Genome-wide transcript profiling with Arabidopsis has identified many genes that are regulated by cold, salt, and drought stress (reviewed in [10]). Similar studies were also conducted with crop plants such as rice, barley, maize, and soybean [11-15]. It was suggested that as many as 30% of the genes in the Arabidopsis genome may be affected by abiotic stress at the transcript level [16]. Some of these genes can be activated by multiple stresses and also by the stress hormone abscisic acid (ABA). Generally, more genes are up-regulated than downregulated [10,17]. This is also true for gene expression in response to ABA. Using the Agilent long-oligo chips, our microarray assay with Arabidopsis seedlings treated with ABA found that over 2000 genes were up regulated by more than 2-fold, whereas about 500 genes were down regulated (unpublished). The products of some of these stress-inducible genes may play roles in stress signaling and stress tolerance [5,7,18,19]. These include, for example, enzymes that function in the biosynthesis of compatible solutes (osmolytes) or either directly in detoxification of reactive oxidants or in the biosynthesis of antioxidant compounds, ion transporters, ABA biosynthetic enzymes, etc. The products of some other genes may also have protective roles against stress damages yet their modes of action are unclear. These are mainly the late-embryogenesis-abundant protein (LEA)-like proteins [2]. However, some stress-regulated genes may not play a primary role in stress response. Their induction may be merely a consequence of the stress and stress injuries [20]. In some cases, genes physically associated with certain key stress-induced genes in a chromatin region may be regulated by stress, although these genes may not be related otherwise. One example is the UFC (upstream of FLC) gene [21]. FLC is a flowering repressor whose transcript level is down regulated by long-term cold treatment (e.g., vernalization). Interestingly, UFC is similarly regulated by vernalization yet it does not relate to FLC either in sequence or in function. They are merely neighboring genes on the same chromosomal region. This suggests that chromosome location may have a strong influence on the induction of certain genes. 3. AN OVERVIEW ON STRESS SIGNAL TRANSDUCTION Signal transduction is required for many cellular activities and their coordination. Some signal transduction processes are simple but most others are complex, involving multiple components and occurring in a time and space-dependent



manner. Generally, signal transduction starts with the perception of a stimulus by a specific cellular molecule(s). These sensors or receptors may differ in their molecular identities, modes of signal perception and output, as well as subcellular localizations. In plant cells, it is also common for receptor activation to result in the generation of second messengers, so called because they represent intracellular signals being translated from the primary external signal. These intracellular messengers are interpreted further by other signaling component(s) and result in the activation of downstream pathways that may have multiple outputs. These pathways usually involve reversible protein phosphorylation. Protein phosphorylation could lead to, among others, the activation of transcription factors that induce the expression of stressresponsive genes. Signal transduction often requires additional components that recruit and assemble signaling complexes, target signaling molecules, and regulate their lifespan. In many cases, these components themselves are also regulated by the signaling pathways that may have been initiated from the same stress signals. Here we refer to these components collectively as signaling partners. Figure 1 depicts a genetic signaling pathway that can serve as a framework for anchoring many of the individual signaling components that are increasingly being reported in the literature. 4. SIGNAL TRANSDUCTION COMPONENTS 4.1. Receptors 4.1.1. Complexity of abiotic stress as signals Receptors are the molecules that first perceive stress stimulus and then relay the signal to downstream molecules to initiate the signal transduction pathway. However, it is not an easy task to find these receptors. Many of the abiotic stress signals are complex in their nature. They may not simply be physical or chemical signals but rather, a mixture of several favours. For example, low temperature may induce both osmotic stress and mechanistic stress. Drought, conditioned by decreased water potential in the soil, may involve osmotic stress, ionic stress, a mechanistic signal, and heat stress in some cases. Very likely, each of these stress attributes may have different weights with regard to the plant status or the severity of the particular stress in question. Thus, a simple water shortage in the soil may in fact impart very complex and different information to the plants. One can also expect that there may be multiple cellular sensors to perceive a stress signal or one attribute of the signal. The complex nature of abiotic stress as signals and the redundancy of their perception machinery pose great constraints for the identification of cellular machinery that perceives abiotic stress.




Examples of components

Examples of Signaling partners

Stress Sensors Ca 2+

2 nd signaling molecules

Ion channels, histidine kinases, GPCR, RLK ROS, InsP, ABA

Phosphoprotein cascades

CDPK, MAPK, Protein phosphatase

Transcription factors

AP2/ERF, bZip, Zn finger, bHLH, MYB

Stress-responsive Genes Responses

Enzymes or components in protein lipidation, glycosylation, sulfation, methylation, and ubiquitination; cytoskeletonassociated proteins, vesicle trafficking components; scaffolds & adaptors

LEA-like, antioxidant & osmolyte synthetic enzymes/transporters Stress tolerance, growth arrest, or cell death

Figure 1. A conceptual signal transduction pathway for drought, cold, and salt stress in plants. Examples of signaling components in each of the steps are shown. It should be noted that none of the indicated receptor components has been confirmed as a stress sensor. Secondary signaling molecules can cause receptor-mediated Ca2+ release (indicated with a feedback arrow). Examples of signaling partners that modulate the components in the main pathway are also shown. These partners can be regulated by the main pathway. Signaling can also bypass Ca2+ or secondary signaling molecules in early signaling steps. GPCR, G-protein coupled receptor; RLK, receptor-like kinase; InsP, inositol polyphosphates. Please refer to the text for other abbreviations.

4.1.2. Putative sensors in stress signal perception Studies in other systems have identified several kinds of receptors that function in stress signal perception. These include receptor-like kinases, two-component receptors, receptor tyrosine kinases, G-protein coupled receptors, iontropic channelrelated receptors, histidine kinases, and nuclear hormone receptors. By sequence hom*ology, most of these receptor families can be found in sequenced plant genomes. However, a few such as receptor tyrosine kinases and nuclear hormone receptors cannot be identified by sequence hom*ology search. Many people thus believe these signaling components nonexistent in higher plants. Because of their stress inducibility or, in a few cases, phenotypes conferred by their regulated expression, receptor-like kinases, two-component receptors, histidine kinases, iontropic receptors, and G-protein associated receptors have each been implicated as potential receptors for abiotic stresses or the stress hormone ABA (reviewed in [9,22]). Despite the importance of identifying stress sensors, research effort to find these receptors has been limited. To date, there has been no convincing evidence to support any of the above-mentioned putative receptors as stress sensors.



Thus, it may be helpful to briefly introduce abiotic stress sensors identified in other systems. In cyanobactieria, histidine kinases were identified as cold-sensors in the activation of selected marker genes [23]. Knockout of these kinases resulted in substantially reduced expression of these genes. In neurons, a TRP Ca2+/cation channel was suggested to be a cold sensor [24]. In fact, similar TRP channels can act as heat sensors as well [25]. However, no TRP channel protein can be found in the sequenced plant genomes using sequence similarity searches. In plant cells, coldinduced Ca2+ influx has been documented as an early response to cold [26]. Manipulations of Ca2+ influx can affect the expression of cold-regulated genes (e.g., [27]). Nonetheless, the calcium channels responsible for this Ca2+ influx have not been identified. As mentioned above, an abiotic stress may initiate multiple signaling pathways in plants. It may be difficult to directly identify stress sensors through genetic analysis, since knocking out one receptor may not significantly affect the stress signaling outputs. Because ABA is involved in abiotic stress signaling, revealing how ABA is perceived certainly will help reveal how stress signals are sensed. Unfortunately, how ABA is perceived is not known either (reviewed in [22]). Current efforts to uncover ABA perception mechanisms mainly focused on putative receptor-linked components or those putative receptor molecules that are regulated by stress or ABA. For example, Arabidopsis heterotrimeric G-protein α subunit GPA1 was suggested to be involved in ABA response in guard cells since gpa1 mutants were insensitive to ABA inhibition of stomata opening and ABA regulation of inward K+ channels, yet it does not function in ABA-induced stomata closure. The gpa1 mutant seedlings lost water more quickly than the wild type [28]. GPA1 interacts with the G-protein couple receptor-like protein GCR1, yet gcr1 mutant was more sensitive to ABA than the wild type [29]. The reason for the opposite phenotypes between gpa1 and gcr1 mutants and the modes of action for both proteins are unclear. In addition to the heterotrimeric G proteins, there are different classes of small G proteins [30]. One of the ROP family Rho GTPases, ROP10, was proved to be a negative regulator of ABA responses in Arabidopsis [31]. Since another ROP related to ROP10 was shown to be associated with CLV receptor kinase [32] and ROP10 was localized to plasma membrane, it was hypothesized that ROP10 may be associated with an ABA perception complex on the plasma membrane [31]. Abiotic stresses also generate second signaling molecules (see below). Receptors for these signals should exist in plants, yet none has been identified. In contrast, receptors for inositol trisphosphate, cADPR and sphingosine 1-phosphate are well characterized in animal systems. 4.2. Second intracellular signaling molecules Several intracellular signaling molecules are involved in stress signal transduction. These include reactive oxygen species, lipid phosphates-derived signals, and cyclic



nucleotides-related signals. In addition, some plant hormones also have the characteristics of secondary signal molecules. 4.2.1. Reactive oxygen species In addition to the reactive species generated during normal photoreactions and cellular biochemical oxidations, plants also produce reactive oxygen species (ROS) during environmental stresses and in response to pathogen attacks (reviewed in [33]). Although these reactive molecules may have damaging effects on cellular membranes and macromolecules, they play important signaling roles in early stages of stress response. These reactive molecules can activate cellular defense mechanisms to mitigate stress damage. Among others, nitric oxide (NO) and hydrogen peroxide (H2O2) are suggested to play roles in ABA signaling and may function in abiotic stress response as well. ABA regulation of stomata closure appears to require the generation of H2O2. H2O2 production is a prerequisite for ABA-induced stomatal closure [34-36]. NAPH oxidase may represent the major source for H2O2 production. Mutations in genes that encode catalytic subunits of NADPH oxidase impair ABA-induced ROS production and the activation of guard cell Ca2+ channels and stomata closure [37]. In plants, nitric oxide can be generated by enzymatic reactions as well as nonenzymatic reactions [38]. Both nitrate reductases and NO synthases (NOS) can contribute to NO generation. It appears that these two kinds of enzymes do not function redundantly since mutations in either enzyme could confer specific phenotypes. For example, loss-of-function mutations in Arabidopsis NOS, AtNOS1, impair ABAinduced NO production and stomata closure [39]. ROS may affect stress signal transduction in the activation of stress-responsive genes [40,41], in particular those that encode enzymes in the biosynthesis of antioxidants or enzymes that directly detoxify reactive oxidative radicals. Then, how does ROS affect stress signal transduction? It was demonstrated that ROS is involved in the regeneration of Ca2+ signals through the activation of Ca2+ channels (reviewed in [42]). These secondary Ca2+ signals could initiate additional signal transduction via Ca2+ mediated pathways [9]. Another route is that reactive oxygen species themselves can directly modify signaling molecules through redox regulation. Molecules with cysteine residues as key active sites could be the targets of redox regulation. These molecules could be potential sensors for ROS [20]. Since tyrosine phosphatases in animals are the potential targets of ROS, and these phosphatases could regulate MAPK cascades, it is believed that MAPK pathways are probably the major pathways mediating ROS signal transduction (see Section 4.5.1). An AGC family protein kinase OXI1 appears to be involved in ROS activation of MPK3 and MPK6 since in oxi1 mutant, activation of both MAPK was compromised [43]. Cellular redox environment may also modulate cell signaling by regulating the activity of other signaling components. One example is the regulation of the transcription activator NPR1 by redox status. A reduced milieu in the cytosol facilitates the inactive NPR1 oligomer to change into an active monomer form. The active NPR1 may target the TGA zinc finger transcription factors and activates PR



gene expression [44]. In Arabidopsis genome, there are several NPR1-like genes, but it is not clear whether any of these genes would regulate stress responses and interact with ABF-like zinc finger proteins. Lipids-derived messengers Membrane lipids may be directly involved in stress response by modulating membrane fluidity or its other physiochemical properties [45]. Yet a more important function of these lipid components is their role in generating intracellular signaling molecules. Lipids and their biogenesis and degradation enzymes play many roles that directly or indirectly regulate or affect plant stress signaling and stress tolerance. For a general discussion of the roles of lipids in cell signaling, readers are referred to a recent review [46]. Some recent advances in lipid signaling of abiotic stress are briefly outlined below. It is known that phospholipids, the backbone of cellular membranes, can serve as precursors for the generation of second messengers in response to abiotic stresses. While the relevant lipid cleaving enzymes are the phospholipases A2, C, and D, the most studied is the phosphoinositide-specific phospholipase C (PI-PLC). Upon activation, PI-PLC hydrolyzes phosphotidylinositol 4,5-bisphosphate (PIP2) to produce two important molecules, diacylglycerol (DAG) and inositol 1,4,5trisphosphate (InsP3). DAG and InsP3 are second messengers that could activate protein kinase C (PKC) and trigger Ca2+ release, respectively. In plants, the role of exogenous InsP3 in releasing Ca2+ from cellular stores has been widely reported [47,48]. Inhibition of PI-PLC activity impairs ABA-induced stomata closure [49] and inhibits osmotic stress-induction of the stress-responsive genes RD29A and COR47 [50]. On the contrary, inhibiting the breakdown of InsP3 may increase the expression of stress-inducible genes. This was demonstrated with transgenic plants overexpressing Arabidopsis inositol polyphosphate 5-phosphatases [51,52] and with loss-of-function or conditional mutation in an enzyme of inositol polyphosphate 1-phosphatase FIERY1 [53,54]. Accumulating evidence suggests that phosphatidic acid (PA) is also involved in the transduction of stress signals. PA is generated by the Phospholipase D (PLD) hydrolysis of phospholipids. In guard cell protoplasts, PLD activity mediates ABA– induced stomatal closure [55]. PA produced by PLDα1 may interact with and inhibit the activity of ABI1, which is a negative regulator of ABA signaling (see below). Consequently, PLDα1 knockout mutants become less sensitive to ABA [56]. Interestingly, PLDα1 interacts with G-protein α GPA1 [57]. Therefore, PLDα1 and GPA1 may in fact function together in controlling aspects of ABA signaling. Knockout plants in another PLD isoform PLDζ are more susceptible to freezing damage whereas its overexpression enhances freezing tolerance [58]. Several other secondary signaling molecules including InsP6, sphingosine1phosphate (S1P), and cADPR were also suggested to regulate ABA responses in guard cells (reviewed in [48]). However, their role in stress signal transduction is unclear.



Phytohormones Upon encountering abiotic stress, plants may alter their growth and development programs. Cell expansion and division may be halted and thus growth generally slower than under normal growth conditions. Longer-term abiotic stress may also affect plant phase transitions. For example, drought stress can promote flowering. These developmental changes imply that abiotic stress may alter the homeostasis of growth regulators. Although plant hormones are not considered as second messengers, the stress hormone ABA acts like one in many aspects: ABA biosynthesis is activated by abiotic stress [59]; ABA mediates many downstream pathways [22]; and ABA can be subjected to long distance transport and play physiological roles at sites distant from where it is synthesized [60]. In addition to ABA, other plant hormones, in particular ethylene and auxin, are involved in ABA and perhaps abiotic stress responses as well. The role of ABA in plant stress responses has long been recognized [12,18]. In guard cells ABA regulates ion channels and promotes stomata closure to minimize transpiration water loss [48]. ABA activates the expression of many stressresponsive genes independently or synergistically with stresses. ABA can inhibit the biosynthesis of ethylene and may also potentially reduce the sensitivity of plants to ethylene [61]. The expression of some aquoporin genes or the activity of these water channel proteins may also be regulated by ABA. With the involvement of ABA in these processes, a general consequence is that plants will adapt to the stress with reduced water potential (so that they could lose less and uptake more water) and consequently, a reduced growth rate. In addition to many physiological and biochemical changes that are mediated by ABA under abiotic stress, ABA may also regulate plant development programs and developmental changes such as root patterning. Our current knowledge in this aspect is limited. 4.3. Ca2+ as an intermediate signal molecule The above-mentioned secondary signaling molecules may activate transient increases in cytosolic Ca2+ [26]. The sources of cytosolic Ca2+ inevitably are either internal or external. Both sources have much higher concentrations of Ca2+ relative to the cytosol. Therefore, the gating of Ca2+ channels is the major means to control Ca2+ transient increase in the cytoplasm. The complex or pumping of Ca2+ into vacuoles (or extracellular space) would be the major route for resetting the signals. Currently, a lot is known about both processes in animal cells but related information in plant cells is limited. Most plant Ca2+ channels may have diverged significantly in primary sequences from those of animal Ca2+ channels. Nonetheless, a putative two-pore Ca2+ channel in Arabidopsis was found to share sequence similarity to a voltage-gated Ca2+ channel in rats [62]. A recent study reported the identification of an ‘extracellular Ca2+ senor’ [63], yet the biochemical functionality and its mode of action for this protein is unclear. Internal Ca2+ could also contribute to stress-induced Ca2+ transients in the cytosol. In animal cells, several Ca2+ channels on ER membranes or other



endomembranes are responsible for transient Ca2+ increases in the cytosol. These include the InsP3 receptors and the cADPR ryanodine receptors. Although InsP3 and cADPR also exist and function in plant cells, their plant receptors have not been identified. Since many cell signaling events use Ca2+ as an intermediate signaling molecule, it is surprising that no Ca2+ channel has been identified in genetic screens that aim to elucidate these signal transduction mechanisms. Given that many putative ion channel genes exist in the Arabidopsis genome, future reverse genetic studies may help to identify potential Ca2+ channels. Cytosolic or organelle Ca2+ concentrations are tightly controlled by various Ca2+ pumps and transporters. These Ca2+ transporters restore cytosolic Ca2+ homeostatasis after various stimulus disturbances. One Ca2+ transporter is the tonoplast Ca2+/H+ exchanger (CAX). These exchangers transport Ca2+ from the cytosol into vacuoles, a major storage of Ca2+ within plant cells. Overexpression of CAX1 resulted in increased freezing sensitivity [64] whereas its knockout mutants exhibited increased efficiency of cold acclimation in that the transcript levels for CBF/DREB1 transcription factor genes (see Section 3.7) and their downstream stress responsive genes were higher in the mutant than in the wild type. These cax1 knockout plants are thus more tolerant to freezing stress [65]. 4.4. Ca2+-binding proteins In contrast to the lack of information on Ca2+ channels in plants, many Ca2+-binding proteins have been identified in plants [66,67]. These Ca2+-binding proteins possess Ca2+-binding motifs that are hom*ologous to those in animal Ca2+ binding proteins. One major Ca2+ binding motif is the so-called EF hand motif, which is conserved across organisms. Major plant Ca2+ binding proteins include calmodulins, SCaBP (SOS3-like Ca-biniding proteins)/Calcineurin B-like (CBL) proteins, and Cadependent protein kinase (CDPK). Arabidopsis SOS3 (Salt-Overly-Sensitive 3) was identified because of the salt hypersensitive phenotypes of the sos3 mutant. SOS3 shares sequence similarity with the calcineurin B subunit (CNB) and animal Ca2+ sensor, although SOS3 does not function as CNB in the activation of calcineurin. Rather, it acts as a Ca2+-binding protein to interact with and activate the AMPK/SNF-like serine/threonine protein kinase SOS2, whose mutation also confers salt sensitivity. The activated SOS2 phosphorylates and regulates ion transporters such as the plasma membranelocalized Na+/H+ antiporter SOS1. This eventually leads to the restoration of ion homeostasis in the cytoplasm under salt stress conditions [68]. In the Arabidopisis genome, there are 9 SOS3 hom*ologs (SCaBP/CBL) and 22 SOS2 hom*ologs (SOS2-like protein kinases -PKS/CBL-interacting protein kinasesCIPK). Individual SCaBP/CBL interacts with PKS/CIPK with different specificities (Gong et al., 2004; Luan et al., 2002). It appears that the various interaction pairs between these two groups of proteins may mediate responses to different abiotic stresses [69,70]. An example is the SCaBP5 and PKS3 interaction that may interpret Ca2+ signatures resulting from ABA or drought stress signals.



Mutations in SCaBP5 or PKS3 confer similar ABA hypersensitive phenotypes in the mutants. In addition, it was found that PKS3 interacts with the ABI2, a type 2C protein phosphatase (see below). ABI2 may negatively regulate the signals perceived by the SCaBP5-PKS3, thus potentially preventing over activation of the downstream signaling pathways. The interaction between PKS3 and ABI2 in this case did not result in detected dephosphorylation or phosphorylation of either partner. It is possible that some other component associated with this complex is the target of ABI2 [71]. More recently, Ohta et al. [72] confirmed this interaction and mapped the protein domain of SOS2 that interacts with ABI2. They found that this interaction is sensitive to the abi2 dominant mutation because the mutated form no longer interacted with PKS3, suggesting that the interaction between PKS kinases and ABI phosphatases may be physiologically significant. Calmodulins have been implicated in several cellular processes through interaction with CaM-binding proteins [67]. The expression of several plant CaM genes is regulated by various environmental stresses such as mechanical stress/touch, cold, salt, or drought stress. Presumably, these CaMs may participate in the transduction of these external stimuli. One of the CaMs, CaM3, was suggested as a negative regulator of COR gene expression, since overexpression of this CaM led to reduced transcript levels of stress-responsive genes RD29A and KIN1 [73]. Consistent with this notion, experimental evidence indicates that a CaM binding protein, AtCaMBP25, may act as a negative regulator of osmotic stress tolerance. Transgenic Arabidopsis plants overexpressing AtCaMBP25 are more sensitive to osmotic stress whereas the antisense plants are more tolerant to salt stress [74]. The involvement of CDPK in stress signal transduction has also been implicated. In addition to stress-inducibility for some of the CDPKs, constitutively active CDPK was demonstrated to regulate stress-responsive reporter gene expression under ABA or stress treatments in protoplasts (Sheen, 1996). Overexpression of a CDPK in rice conferred increased tolerance to cold and salt stress [76]. However, there has been no report showing that loss-of-function CDPK may affect stress signal transduction or stress responses. Other Ca2+-binding proteins or Ca2+-dependent proteins include annexins [77], calnexin and calreticulin. Calnexin and calreticulin may serve as endoplasmic reticulum (ER) chaperones and ER Ca2+ reservoirs. The role of these proteins in stress signaling is unclear. However, plants may have similar ER stress responses as do other eukaryotes [78]. 4.5. Phosphoproteins at the core of stress signal transduction In many signal transduction pathways, protein reversible phosphorylation is the major form of signal relay. The enzymes that catalyze these reversible phosphorylation processes are protein kinases and protein phosphatases. In the Arabidopsis genome, there are over 1,085 protein kinases (cited in [79]) and 112 protein phosphatases [80]. Protein kinases and phosphatases can be divided into several categories based on substrate specificity or on the structure or functional



characteristics. In this section, we present several recent examples on genetic studies of the role of phosphoproteins in stress signaling. 4.5.1. MAPK Aside from its mysterious position in stress signaling, the mitogen activated protein kinase (MAPK) cascades are known to be involved in plant abiotic stress responses. The cascade is characterized by the sequential phosphorylation of a kinase by its upstream kinase in the order of MAPKKK-MAPKK-MAPK. Early studies found that the transcript levels of certain MAPK genes were enhanced by cold and salt stress. Some late studies followed the kinase activities for these proteins and found the activation of MAPK by stress treatments [81]. In several cases, regulated expression of MAPK components was shown to affect stress sensitivity. For example, expression of an active form of a tobacco MPKKK, NPK1, increases freezing tolerance of transgenic tobacco or maize plants [82,83]. Recently, a MAPK cascade in Arabidopsis was suggested to be involved in cold and osmotic stress signal transduction. This cascade consists of the MAPKKK MEKK1, the MAPKK MKK2, and two MAPKs, MPK4 and MPK6 [84]. Salt and cold stresses activate MKK2, MPK4 and MPK6, whereas in mkk2 mutant plants, MPK4 and PMK6 were no longer activated by cold. The mkk2 mutant plants were also sensitive to freezing and salt stress. Transcript profiling revealed that 152 genes were affected by over-expression of MKK2. These include genes for several transcription factors (such as RAV1, STZ, ZAT10, ERF6, WRKY, and CBF2), disease resistance proteins, cell wall related proteins, enzymes involved in some secondary metabolisms and an ACC (1-aminocyclopropane-1-carboxylate) synthase. Interestingly, several auxin-responsive genes were down regulated. Although this MAPK cascade apparently is involved in stress responses and the CBF2 transcript level was higher in the overexpressing plants, none of the CRT/DREB class of stress-responsive genes was significantly affected by this cascade. This is consistent with our previous prediction that MAPK pathways appear to be independent of the pathways that up regulate the expression of the CBF/DREB class of stress responsive genes [9]. In addition, since genes involved in other hormone biosynthesis (ethylene) and responses (auxin) were altered, it will be important to distinguish the direct targets of this MAPK cascade from those that are regulated by altered hormonal and oxidative stress responses. It is known that the ‘cross-talk’ between various MAPK cascades is intensive [81] and that various feedback regulations are also common within some pathways. For instance, MAPK6 had previously been shown to affect auxin signaling and stress tolerance [82], disease resistance [43,85], and ethylene biosynthesis [86]. Similarly, MPK3 was also suggested to affect ABA inhibition of seed germination [87] and pathogenesis signaling [43,85]. Identifying the targets of MAPK cascades may prove to be challenging. 4.5.2. Other protein kinases Certain protein kinases are induced by various abiotic stresses either at the transcript level or at the activity level, implying that they may be involved in transduction of



these stress signals . T here have been several reports presenting evidence that suppression or overexpression of some of these kinases resulted in altered stress responses in transgenic plants. However, genetic studies regarding the in vivo functionality for these kinases have been lacking. An exception is the SOS2 group AMPK/SNF like kinase (see Section 3.4), which was grouped into the SNF1-related kinase subfamily 3 (SnRK3) [79]. Some other members in the SnRK family were also shown to affect stress signaling and stress responses [79]. The protein kinase OST1 functions in the ABA signaling pathway upstream ABA-induced ROS production [88]. OST1 is related to the ABA-activated protein kinase AAPK in Vicia faba [89] and also related to SNF1 protein kinase [90] and was grouped into the SnRK2 subfamily [79]. The ost1 mutants showed reduced response to ABA in stomata closure yet did not change in ABA responsiveness during seed germination. Ost1 activity is activated by ABA but its gene expression is not. Proteins similar to Ost1 also exist in several other plants and were reported to have similar roles in regulating osmotic stress and ABA signal transduction [91,92]. Further genetics and biochemistry studies are expected to reveal the roles of these kinases in stress signaling by defining their targets and modes of action in stress signaling. 4.6. Protein phosphatases Protein phosphatases dephosphoryate phosphoproteins and thereby attenuate the function of protein kinases. Protein phosphatases can be classified by their substrate specificity as serine/threonine phosphatases, tyrosine phospahtases, and dual specificity phosphatases. Among them, serine/threonine phosphatases are the largest group of phosphatases in plants. According to their sequence (structure) characteristics and cation requirements, serine/threonine phosphatases can be classified further into PP1, PP2A, PP2B, and PP2C. Among these phosphatases, some PP2C, PP2A, PTP, dsPPase have been implicated in ABA or stress signal transduction [93,94]. The best-known example is the PP2C involvement in ABA signal transduction. Early genetic studies using the inhibitory effect of ABA on seed germination identified the ABA-insensitive 1 (ABI1) and ABI2, two hom*ologous 2C type phosphatases (reviewed in [22]). However, due to the dominant nature of both mutations, their roles in ABA signaling were not clear. Mutation analysis and reporter-gene assays in protoplast systems suggested that these ABI may function as negative regulators of ABA signaling [95]. Consistent with this notion, recessive intragenic revertants of abi1 exhibited hypersensitivity to ABA in seed germination and vegetative growth [96]. Although ABA hypersensitive phenotypes for loss-of-function abi1 and abi2 mutants have not been reported, the discovery of other PP2C as negative regulators of ABA signaling [97,98] supports the idea that some PP2C may function as negative regulators of ABA signaling. Following the isolation of the dominant abi1-1 and abi2-1 mutants, many researchers used these mutants in their studies of abiotic stress signaling and plant stress tolerance. It is clear that ABA or stress induction of many ABA and



stress-regulated genes are impaired in abi1 [99] or abi2 mutants (reviewed in [22]). Further studies using both mutants have found that abi1-1 and abi2-1 have defects in reactive oxygen species generation or their regulation on ion channels. The abi1-1 mutants are impaired in ABA-induced ROS production whereas abi2-1 guard cells are defective in H2O2-activated Ca2+ channel regulation [35]. To reveal the functionality of ABI1 and ABI2, it is essential to identify their targets. In yeast two-hybrid assays ABI1 interacts with the homeodomain transcription factor AtHB6 [100]. ABI1 and ABI2 also interact in vitro and in vivo with the SOS2 class of protein kinases [71,72] (see above sections). Some signal molecules such H2O2 and fatty acids were shown to bind to ABI1 or other PP2C (reviewed in [93]). ABI1 may also be regulated by PA derived from PLDα hydrolysis of phospholipids. PA binding of ABI1 inhibits ABI1 phosphatase activity and therefore will activate ABA signaling in response to ABA [56]. Interestingly, Zhang et al. [56] reported that ABI1 was predominately localized in the cytoplasm but tended to be relocated to plasma membrane in response to ABA treatment. It should be noted that PA is generated upon ABA treatment and is also membranelocalized. Subcellular localization of ABI1 and ABI2 were not reported before. If ABI1 does not localize in the nucleus where AtHB6 is found [100], the interaction between AtHB6 and ABI1 may not occur in vivo. Previous pharmacological studies suggested that PP2A might be involved in cold stress signaling [101]. Recently, PP2A was shown to play roles in ABA activation of slow anion channels in guard cells because the rcn1 mutant exhibited ABAinsensitivity to ABA in stomatal closure and was impaired in slow anion channels regulation by ABA [102]. RCN1 encodes the regulatory subunit of PP2A. Because RCN1 is involved in response to ethylene and auxin [103,104], it is not clear whether the role of RCN1 in ABA signaling is the consequence of the regulation of an ABA signaling component(s) by PP2A or a result of the complex interaction between different plant hormones. 4.7. Transcription factors in stress signaling Presumably, the targets of some protein kinases will be transcription factors that upon activation will bind to cis-elements in the promoters of stress-responsive genes and thus activate their transcription. Transcription factors may themselves be regulated at the transcription level by other upstream transcription factors. These further upstream transcription factors are often in a constitutively active state but are contained by repressors or held physically separate from their target genes (e.g., in cytoplasm or inaccessible to the target regions within the nucleus). Regulation of these transcription factors is therefore an important way to control gene expression. Common means for the release of repression include conformation changes by protein phosphorylation, degradation by ubiquitination, and trafficking between subcellular localizations. Protein kinases could play roles in all these processes, yet examples in plants are still very rare. Nonetheless, a lot has been learned regarding gene activation by transcription factors during abiotic stress signal transduction.



Several classes of transcription factors are involved in the activation of stressresponse genes in plants. These include the AP2/ERF (ethylene responsive element binding factor), Zn finger, basic leucine zipper (bZIP), basic helix-loop-helix (bHLH), MYB, and NAC transcription factors. The CBF/DREB transcription factors belong to the AP2/ERF class and have been studied in detail. These transcription factors bind to the C-repeat element (CRT)/dehydration-responsive element (DRE) in the promoters of many stress-responsive genes [3,19]. Nonetheless, CBF/DREB may not be the sole transcription factors in the regulation of CRT/DRE genes. A homeodomain transcription factor, HOS9, regulates cold signal transduction and cold tolerance through a pathway independent of the CBF/DREB transcription factors [105]. Because of their functional redundancy, null mutation in a single CBF/DREB transcription factor may not necessarily give rise to a visible phenotype. On the other hand, several experiments demonstrated that overexpression of CBF/DREB transcription factors could lead to an enhanced expression of stressresponsive genes and increased tolerance to various abiotic stresses [3,19]. Because CBF/DREB transcription factor genes are also induced by stress, upstream transcriptional activators must exist. Recently, it was suggested that CBF2 probably is a negative regulator of other CBF genes, since in cbf2 knockout mutant, the transcript levels of CBF1 and CBF3 were slightly higher than in the wild type, and the cbf2 mutant seedlings were more resistant to freezing stress [106]. Another putative transcription factor for CBF/DREB1 genes is ICE1. A dominant mutation in ICE1 resulted in impaired cold-stress regulation of CBF genes, whereas overexpression of ICE1 increases cold-induced CBF and the downstream gene expression. These transgenic plants are also more tolerant to chilling and freezing stress [107]. Several other putative signaling components that regulate the CBF/DREB class of transcription factors were identified in genetic screens for altered stress-inducible RD29A::LUC (luciferase) reporter gene expression. Mutation in the HOS1 gene resulted in increased stress-responsive gene induction by cold. HOS1 is a novel protein containing a RING finger domain that potentially participates in protein degradation. Since hos1 mutant seedlings had higher expression of CBF transcription factor genes, it is hypothesized that HOS1 may target positive regulators CBF transcription factors for proteolysis. Other potential regulators include FRY1/HOS2 [54], FRY2/CPL1 [109], and LOS4 [110]. FRY2 encodes a novel RNA polymerase II C-terminal domain (CTD) phosphatase [109,111,112] and may function in the regulation of transcript elongation. FRY1 encodes a bifunctional enzyme with both inositol polyphosphate 1-phosphatase and nucleotidase activities [53]. Both fry1/hos2 and fry2 mutants had higher transcript levels of several CBF transcription factor genes and higher level induction of stress-responsive genes [53,54,109], whereas los4 had a lower transcript level of CBF genes [110]. Because of the nature of these proteins, fry1/hos2, fry2/cpl and los4 may indirectly regulate the transcription of CBF either through upstream signaling pathway regulation or through regulation of the transcription machinery under abiotic stress.



4.8. Chromatin remodeling factors Because genes are packed in chromatins, remodeling of chromatin structure to allow positive transcriptional regulators access to the genes is thus a critical step toward gene activation. It is conceivable that stress signal transduction involves components in chromatin remodeling. An example in this regard is the activation of the yeast High Osmolarity Glycerol 1(Hog1) pathway. Upon osmotic stress, a MAPK pathway is activated and leads to the phosphorylation of the MAPK Hog1. Activated Hog1 is recruited to specific promoter regions by transcription factors. Hog1, once bound to the promoter complex, then recruits histone deacetylase Rpd3 to deacetylate histone and activate osmoresponsive genes [113]. Currently, little is known about the regulation of chromatin remodeling by most abiotic stresses except for low temperature. Many plants in the temperate region require an exposure to prolonged low temperature (winter) to promote flowering in the spring, a process referred to as vernalization. In Arabidopsis, vernalization involves the down regulation of the flowering suppressor Flowering Locus C (FLC). FLC has a dosage repressing effect on flowering time. Vernalization modifies the FLC locus into a repressed state by histone methylation and therefore promotes flowering transition [114]. It should be noted, however, that vernalization and cold acclimation are two different processes [115]. Plants respond to them differently both in terms of gene expression and physiological consequences. 4.9. Posttranscriptional regulation in stress signaling Gene regulation could occur at the level of transcription, posttranscription, translation, and posttranslation. Current studies of stress gene regulation are mainly focused on the transcription level. Although other processes of gene regulation are also important, it is only until recently that the importance of posttranscriptional regulation of stress responsive genes has become evident. Particularly, genetic studies of ABA and stress signal transduction have demonstrated that aspects of mRNA processing are critical for stress and ABA signal transduction. In screens for components that affect the activation of the RD29A::LUC reporter gene, several mRNA processing factors or RNA-binding proteins were isolated. The SAD1 (Supersensitive to ABA and Salt 1) encodes a Sm-like U6 small ribonucleoprotein (snRNP) that is required for mRNA splicing and export. The sad1 mutant plants are hypersensitive to ABA and osmotic stress in gene expression, seed germination, and vegetative growth. The mutant plants are also defective in ABA biosynthesis because drought regulation and self-regulation of ABA biosynthetic genes are impaired in the mutant [59,116]. A second component is the FRY2/CPL1 RNA Pol II CTD phosphatases [109,111,112]. FRY2/CPL1 contains two dsRNA binding domains, suggesting that structured RNA may regulate the FRY2/CPL1 activities [109]. In the same screen, a RNA helicase, LOS4, was found to be required for cold acclimation and cold-regulated gene expression [110] (see Section 3.7). All these studies indicate a potential role of RNA processing in stress and ABA signal transduction.



Using different approaches, several other groups have discovered similar components functioning in ABA signal transduction. ABH1 (CBP80) is an mRNA cap binding protein. The abh1 mutant was isolated by its hypersensitivity to ABA during seed germination. The abh1 guard cell ion channels are also hypersensitive to ABA [117]. Because of its enhanced sensitivity to ABA in guard cells, abh1 plants can withstand water shortage for a longer time than the wild type plants. Mutation in another cap binding protein, CBP20, which is in complex with ABH1, confers phenotypes similar to ABH1 [118]. CBP80 and CBP20 are single copy genes and therefore, their mutations confer pleiotropic phenotypes such as small statue and serrated leaves. The abh1 mutation also suppresses the late-flowering phenotype conditioned by mutation in FRIGIDA [119]. Other RNA-binding proteins that potentially affect ABA signaling include HYL1 and AKIP. The hyl1 mutant is hypersensitive to ABA during seed germination, and also hypersensitive to cytokinin, auxin, glucose, and salt and osmotic stress[120]. HYL1 is a dsRNA binding protein and appears to affect the levels of several miRNA [121,122]. The ABA-activated protein kinase (AAPK) interacting protein AKIP is similar to heterogeneous nuclear RNA-binding protein A/B in animals [123]. AKIP probably functions in the targeting or trafficking of certain mRNA [123] and may also regulate the stability of mRNA species that encode ABA signaling components. Another group of molecules that can potentially regulate stress signaling and also plant developmental adaptation to stress is small RNA. Small endogenous RNA such as micro RNA (miRNA) and short interference RNA (siRNA) may regulate the transcript stability of some stress signaling components. The biogenesis of some of these small RNA may also be regulated by stress or ABA [124]. 4.10. Regulation of stress signaling components by protein modifiers The above-mentioned components are directly involved in stress signaling. In many cases, however, their roles in stress signaling may be regulated by other components that are not directly involved in the signal relay. Protein modifiers that are responsible for protein lipidation, glycoslation, methylation, sulfation, and ubiquitination regulate protein targeting, activity and longevity. Some of these processes are known to affect abiotic stress signaling. Protein lipidation facilitates membrane localization of the modified proteins. Prenylation (including farnesylation and geranylgeranlylation) is particularly required for signal transduction that involves small GTPases. Although the detailed plant pathways that are regulated by prenylation are unclear, it is known that ABA signaling requires that some of its components be modified by prenylation. Mutations in subunits of protein farnesyl transferase or geranylgeranyl transferase made the mutant plants hypersensitive to ABA in seed germination and stomatal regulation [125,126]. Nonetheless, the regulation of the stress-responsive genes NCED3 and ABA1 in era1 mutant does not appear to be hypersensitive to ABA or NaCl [127], suggesting that stress and ABA activation of these genes may not require ERA1.



Myristoylation is another form of protein lipidation. Several proteins in stress responses are known to be modified by myristalation. These include CDPK [128,129] and the Ca2+-bindign protein SOS3. Myristoylation is required for SOS3 function in salt tolerance [130]. Other protein modification processes such glucoslyation, sulfation, and nitrosylation may also affect stress signal transduction, but currently there is little experimental information to confirm this hypothesis. An Arabidopsis mutant defective in an oligosaccharyltransferase that potentially affects protein glycosylation is more sensitive to salt and osmotic stress [78]. Protein ubiquitation is often used by cells to target signaling proteins for degradation, thereby regulating signal transduction. The role of proteolysis in cell signaling was established for several processes such as light signaling, hormone (auxin, ethylene, GA, and ABA) signaling and signaling for pathogenesis [131,132]. Although information regarding the role of protein ubiquitation in stress signaling is limited, its role in ABA signaling is now well documented. Ubiquitination was found to regulate ABA signaling component ABI5 during seed germination and early seedling development. ABI5 is a bZip transcription factor whose mutation confers insensitivity of seed germination to ABA inhibition. Following seed germination, ABI5 is ubiquitinated and the germinated embryos established as seedlings. ABA can stabilize ABI5 and therefore prevent seed germination and seedling establishment [133]. When the 26S proteasome regulatory particle subunit RPN10 was mutated, ABI5 was stabilized and, therefore, the rpn10 mutant seeds are hypersensitive to ABA inhibition of seed germination [134]. Ubiquitination process involves the ubiquitin activating (E1), conjugating (E2) and ligating enzymes (E3). The SCF (Skp1/Cullin/F-box/Rbx1/2) complexes represent a major type of E3 ubiquitin ligases. F-box proteins in the SCF complexes may define substrate specificity. In Arabidopsis, there are about 700 putative F-box proteins [132]. One F-box protein has been suggested to be involved in ABA signal transduction since the knockout mutant became insensitive to ABA during seed germination [135]. Protein ubiquitination also removes denatured or unfold proteins. These unnatural proteins may become abundant under abiotic stress conditions. Chaperone proteins could restore some of these proteins to their native state [136]. Abiotic stress induces the expression of several heat shock proteins (Hsp). However, the role of these Hsp proteins and other chaperones in stress signaling is not very clear. In animal cells, an important role for some of these chaperones is the assembly of hormone receptor complexes. In plants, all the chaperone proteins such as Hsp90, Hsp70, immunophilins, cyclophilins, TPR (tetratricopepitide repeat) domain adaptor proteins exist, yet no obvious nuclear hormone receptors are found in completely sequenced Arabidopsis and rice genomes. The role of these proteins in stress signaling will await discovery in future studies. 4.11. Role of scaffolds and adaptors and vesicle trafficking in stress signaling Signal transduction often requires the assembly of protein complexes. This involves recruiting, organizing, and anchoring of individual components. Specific proteins are evolved to play this scaffold and adaptor roles. These proteins usually contain



conserved protein-protein interaction domains. Although the role of scaffold protein in signaling is expected, there has been little information regarding these proteins in plant stress signaling. Other proteins with a physical role in supporting signaling molecules or their trafficking include cytoskeleton and its associated proteins. Cytoskeleton reorganization was suggested to play roles in early steps of cold signal transduction [45,137] Vesicular trafficking is required for many signal transduction processes. In yeast cells, the barley stress and ABA-induced protein AtHVA22 interacts with vesicle trafficking component, which has high hom*ology with the Arabidopsis RHD3 protein, a protein involved in root hair development [138] and trafficking between ER and Golgi body [139]. Previously, it was shown that drought and ABA affect root hair development in Arabidopsis [140,141]. It is not clear whether this process requires RHD3 or whether RHD3 is defective in drought responses. Components in other aspects of vesicle trafficking, such as syntaxin-like proteins, are also implicated or demonstrated in ABA and osmotic stress response [142,143]. Rab GTPases that regulate vesicle trafficking [144] may also indirectly affect plant abiotic stress signal transduction and stress tolerance. Indeed, Mazel et al. [145] reported that overexpression of AtRabG3E resulted in increase tolerance to salt stress. 5. SIGNAL TRANSDUCTION PATHWAYS AND NETWORK INTEGRATION In the previous sections, we presented an overview on individual components involved in stress signal transduction. Needless to say, there are many more components to be discovered, and some of them (such as stress signal receptors) are essential to understanding signal transduction. However, with more and more components being described, an important next task will be to sort out the pathways that integrate these different components. Since individual pathways interact with one another at various levels, the signal pathways actually constitute a signaling network. While integrating these different pathways, one thing often discussed is the interaction (cross-talk) or specificity of various pathways. Evidently, many genes can be activated by multiple stresses and by the plant hormone ABA (see previous sections). This could result from pathway interactions at any signaling steps (Figure 1). For instance, different stresses many share similar intrinsic attributes (Section 3.11). An obvious example is that drought and salt stress both lead to osmotic stress. In this case, the signaling pathway activated by osmotic stress would likely be shared by both drought stress and salt stress. On the other hand, the ionic stress generated by Na+ would be specific to salt stress. Additional layers of interactions could occur at the generation of second signal molecules (see Section 3.2). Particularly, various stresses may affect the biosynthesis of and response to various plant hormones such as ABA and ethylene. Abiotic stresses as well as biotic stress also generate reactive species. The signal transduction pathways initiated by a common secondary signaling molecule would be similar in terms of the usage of signaling components and the outputs of the signaling pathways, even if their primary signals are quite different.



Indeed, one reason why so many stress-inducible genes are activated by drought and salt stress (as well as by low temperature) is that all these stresses activate the biosynthesis of ABA [117]. The expression of certain stress-responsive genes appears to require ABA for their activation by stress, since osmotic stress no longer activates the expression of these genes in ABA deficient mutants [146]. Consistent with the observation that short-term cold stress has relatively little effect on ABA biosynthesis, the activation of stress responsive genes by cold was not obviously affected in the ABA biosynthetic mutants [127,146]. As a result, quite a few coldspecific components were identified genetically (e.g., ICE1, HOS1), whereas drought, salt, or ABA specific signaling components are rarely isolated in genetic studies. Transcript profiling also indicates that more than half of the droughtresponsive genes are induced by salt stress, whereas only about 10 percent of drought-inducible genes are induced by cold stress [3]. Additional interactions between different stress signal pathways can occur at the level of protein reversible phosphorylation. Many protein kinases and phosphatases can be induced or activated by various abiotic stresses or ABA treatment. Their substrates may also play diverse roles in stress signaling. An example is the MAPK MPK6 (see Section 3.5.1). On the other hand, downstream signaling components such as transcription factors appear to have relatively more signaling specificity. For instance, there are cold specific transcription factors (CBF1 to CBF3), drought/ osmotic stress-specific transcription factors (DREB2), and ABA-specific transcription factors (ABF) [147,148]. Nonetheless, many stress-responsive genes have multiple cis-regulatory elements in their upstream regulatory regions. These cis-elements may collectively increase the signaling output and also underline the basis for crosstalk among pathways. For instance, The CRT/DRE element was suggested to function also as an ABRE coupling element in the RD29A promoter [149]. Therefore, abiotic stress signal transduction pathways are more like an intertwined network. Signal specificity occurs at the local and at the module levels rather than at the global level. Thus, for abiotic stresses, signaling pathway interaction is the rule rather than the exception. ACKNOWLEDGEMENTS We thank Christine Ehret for critical reading of the manuscript. Research at the author’s laboratory has been supported by the United State Department of Agriculture-National Research Initiatives (Grant #2004-02111) (to L.X) and Bundesministerium fur Wirtschaftliche Zusammenarbeit und Entwicklung (BMZ), the Japanese Ministry of Foreign Affairs (MOFA) (to M.I).

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AKIHIRO UEDA, SHIRO MITSUYA AND TETSUKO TAKABE1 Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan 1 Correspondence author e-mail: [emailprotected]

Abstract. Plants regulate expression of a set of genes in response to environmental stresses. Hence, it is important to decipher the information on comprehensive expression analysis under stress condition. We have studied salt-inducible genes in barley by differential display and the function of some candidates using heterologous expression system. Total 218 and 102 cDNA clones were identified as a salt-inducible gene in barley roots and leaves under salt stress, respectively. Among these, transgenic Arabidopsis overexpressing peroxisomal ascorbate peroxidase or proline transporter showed tolerance toward heat or salt stress. Using barley salt-responsive genes, we have also fabricated barley custom cDNA microarray system to monitor the transcriptomes in barley and rice. Comparative analysis reveals the differences in gene expression pattern between the two plants during the initial phase of salt stress. Especially, divergent responses were observed in expression profiles involving in osmoregulation and ion homeostasis. Furthermore, transcript of methionine synthase is increased in barley, but not in rice. This is identical to abundance of methionine synthase protein that examined by Western blot analysis. Thus, direct comparison in transcriptome is useful to narrow the differences in the two plants, and give information on genetic improving of plant stress tolerance.

1. INTRODUCTION Plants have developed the adaptation mechanisms to changes in their surroundings during a long evolutional process. Under environmental stress conditions (high salinity, drought, high and low temperature or light, UV, etc.), plants show the ingenious adaptations at physiological level, accompanied with the change of various gene expressions. For example, biosynthesis of glycinebetaine (betaine) or proline, a well-known osmoprotectant, is triggered by salt or drought stress, and expression level of the gene encoding betaine aldehyde dehydrogenase (BADH) or pyrroline-5-carboxylate synthetase (P5CS), a component of betaine or proline synthetic pathway, is also increased [1-3]. Stress-mediated modification in gene expression pattern is achieved by components of a signal transduction pathway, such as the sensor proteins [4] or transcriptional regulator [5]. It was estimated that 31 Ashwani K. Rai and Teruhiro Takabe (eds.), Abiotic Stress Tolerance in Plants, 31-45. © 2006 Springer. Printed in the Netherlands.



Arabidopsis has 1,533 transcriptional regulators in genome and it accounts for 5.4% of the whole genes [6]. The ratio of transcriptional regulator in Arabidopsis genome is larger than that of C. elegans (3.5%), D. melanogastor (4.5%) or S. cerevisiae (3.5%). Some classes of transcriptional regulator, AP2/EREBP, WRKY, ARFAux/IAA and Dof, are specific to plants [7], and plants seem to have the unique transcriptional system. Including these transcriptional regulators, it is important to study global changes of gene expression in response to environmental stimulus for improvement of plant stress tolerance. Recently, by the advancement of molecular biology, various approaches are developed to identify the candidates that are differentially regulated at transcript level. cDNA subtraction and differential screening are often used to obtain stressinducible genes. With the refinement in sensitivity of detection, differential display is also the effective tool to get differentially expressed genes [8-10]. Since differential display does not need expensive equipments, it is widely applied to various purposes from microorganisms to plants and animals. On the other hand, cDNA microarray enables to handle more than several thousand cDNA clones at once for genome-wide expression analysis [11]. Serial analysis of gene expression (SAGE) is also developed for the large scale and quantitative expression analysis that is sequencing the arrayed short tags derived from 3’-UTR of cDNA [12]. Although these have both merits and demerits, many reports utilized above mentioned approaches are published for identification of stress-responsive genes. Crop productivity is irreversibly inhibited by environmental stresses, and especially, salt stress is one of the serious problems in world agriculture. Salt stress causes both water relation and ion homeostasis. For improving salt tolerance in plants, many approaches of genetic engineering were made attempts until now. It was reported that the intensification in ability of synthesis of osmoprotectant or exclusion sodium ion from cytosol are effectively to improve salt tolerance in Arabidopsis or rice [13-17]. One of the effective strategies is to invest the new traits derived from tolerant plants into salt-sensitive plants. In such sense, a model crop plant, rice, is a good target to invest salt tolerance with genetic information of closely related and salt-tolerant plants, such as barley, wheat, or another monocotyledonous plants. To obtain useful candidates for improving salt tolerance in plants, we have examined salt-inducible genes in barley leaves and roots by differential display and the role of some genes was identified. Then, we have dissected expression profiles of barley and rice under salt stress by cDNA microarray that was fabricated using barley salt-responsive genes and compared their transcriptomes with physiological responses. 2. SCREENING SALT-INDUCIBLE GENES IN BARLEY BY DIFFERENTIAL DISPLAY Differential display is one of the powerful approaches to identify the differentially regulated genes between two samples. Firstly, Pardee and Liang developed differential display RT-PCR technique combined with oligo-dT primer and short arbitrary primers [8]. Some variations of differential display method were reported,



such as the simple version with RAPD primer [18], utilization of fluorescencelabeled primer [19] and restriction fragment-coupled version [20]. Basically, differential display is one of the mRNA fingerprintings and consists of two steps, reverse transcription and PCR with arbitrary primer. Specifically expressed genes are partially amplified by PCR, and the resulting DNA fragments are easily subcloned and sequenced. One of the points is which primers should be used, oligodT or random primer for reverse transcription, and what kind of and how many arbitrary primers for PCR (10-12 mer). Logically, emergent frequency of 10 mer sequence of arbitrary primer is less than 1,000 kbp in target cDNA. Size of cDNA amplified by PCR is usually ranged from 100 bp to 2,000 bp, suggesting probability of annealing to cDNA with arbitrary primer is quite low. However, mismatch annealing would actually occur due to the lower annealing temperature (approx. 40oC). This complexity is still argumentative [21]. In comparison with other approach to identify the differentially expressed genes, differential display has the virtue of high sensitivity due to application of RT-PCR. On the other hand, sometimes, false clones might emerge because of inaccurate PCR-amplification. Therefore, expression level of positive candidates obtained by differential display should be confirmed by alternative approaches, such as RT-PCR or Northern blot analysis. 2.1. Salt-inducible genes in roots Plant root is the tissue that primarily perceives salt signaling from soil. During imposition of salt stress, root cells are exposed to high salinity environment, hence dynamic changes in gene expression might occur in roots under salt stress. Differential display was performed with 480 species of RAPD primers (random 12 mer) and first strand cDNAs transcribed from poly (A)+ RNA using random hexamer. Detailed information was described in previous report [10]. Total 218 saltinducible genes were obtained by differential display using 6 days stressed barley roots (100 mM NaCl for 3 days, and then 200 mM NaCl for 3 days) (Table 1). Of these, 133 cDNA clones have similarity to known protein such as the components of signal transduction (26 genes), membrane protein (17 genes), cytochrome P450 (16 genes), sugar, amino acid, C/N relations (16 genes), stress tolerance (13 genes), RNA functions (11 genes), proteases (4 genes) and others (30 genes). These includes some of typical stress-responsive genes, phosphatidylinositol-4-phosphate-5-kinase (PIP5K), mitogen activated protein kinase (MAPK), heat shock protein (HSP), polyubiquitin, etc. It was reported that some of these genes is useful to improve salt tolerance by transgenic approach, such as inorganic pyrophosphatase [22], proline transporter (HvProT) [23], glutathione reductase [24], trehalose-6-phosphate synthase [25] and translation initiation factor [26]. Many novel genes are identified as a saltinducible candidate in plants, such as AMSH (Associated Molecule of SH3 domain of STAM), putative SET1 (Su(var)3-9, Enhancer-of-zeste, Trithorax) -domain protein, splicing factor, nonsense-mediated mRNA decay trans-acting factor, apoptosis protein Ma-3, and so on. By Northern blot analysis, expression of approximately 70% of salt-inducible genes obtained from stressed roots is



up-regulated in roots but not in leaves. This indicated different regulation system of gene expression in roots and leaves in response to salt stress. Interestingly, it was shown that transcripts of HvProT and aldehyde oxidase, catalyzes the last step for ABA biosynthesis, are localized in root cap cell [3, 27]. Function of root cap cell is not clear under salt stress although it is expected to play roles as the place of plant hormone biosynthesis and the sensors for gravitropism and hydrotropism, and secretion of various compounds into soil. Further analysis needs to be done to show the function of root cap cell under salt stress. Table 1. Up-regulated genes in barley roots under long-term salt stress. Category Number Description Signal transduction 26 Serine/ threonine protein kinase (6), Receptor protein kinase (6), SET-domain transcriptional regulator (2), SCARECROW (2), Protein phosphatase (2), Transcription factor (2), MAPK, AMSH, Casein kinase, etc. Membrane protein 17 ABC transporter (7), Inorganic pyrophosphatase (3), Amino acid permease (2), Proline transporter, Sugar transporter, etc. Cytochrome P450 16 CYP99A1 (5), P450 monooxygenase (5), CYP72A1 (2), CYP71C4, Trans-cinnamic acid hydroxylase, etc. Metabolism 16 Sucrose synthase (2), Phosphogluconate dehydrogenase, Fd-GOGAT, PEPCase, GAPDH, etc. Stress tolerance 13 HSP90, HSP70, Trehalose-6-phosphate synthase, Glutathione reductase, Phosphoethanolamine-N methyltransferase, etc. RNA functions 11 Nonsense-mediated mRNA decay trans-acting factor (2), Splicing factor, Translation initiation factor, Elongation factor, etc. Protease 4 Subtilisin protease (2), Clp protease, Aspartic proteinase Others 30 GcpE protein (4), Oxalate oxidase (3), Proline rich protein (2), Kaurene synthase (2), Rf2 nuclear restore protein (2), Apoptosis protein Ma-3, Dynamin, Tubby like protein, Brassinosteroid insensitive 1 gene, Mannose/glucose-binding lectin, etc. Unknown 85

2.2. Salt-inducible genes in leaves Leaf salt-inducible genes are screened under short- or long-term salt stress. At 30 min of 200 mM NaCl stress (short-term), 60 cDNA clones were obtained, including the genes related to signal transduction (4 genes), membrane protein (4 genes), RNA functions (4 genes), defense (4 genes), cell wall biosynthesis (3 genes), photosynthesis (2 genes), protease (1 gene), others (16 genes) and function unknown protein (22 genes) (Table 2). On the other hand, smaller number of salt-inducible genes (42 candidates) was identified by long-term salt stress treatment (100 mM NaCl for 3 days, and then 200 mM NaCl for 3 days) [28, 29]. Calcium dependent protein kinase (CDPK) was up-regulated under both short- and long-term stress conditions, suggesting that CDPK would play important roles for stress signaling during high salinity condition. Actually, it was revealed that overexpression of



Table 2. Up-regulated genes in barley leaves under short- or long-term salt stress. Category Number Short-term salt stress Signal transduction 4 Membrane protein


RNA function


Defence Cell wall Photosynthesis Protease Others

4 3 2 1 16



Long-term salt stress RNA function 6 Signal transduction


Membrane protein


Amino acid synthesis 4 Protease


Defence Others

1 9



Description Calcium dependent protein kinase, Serine/threonine protein kinase, Response regulator, Elicitor inducible protein kinase Sugar transporter, Vacuolar H+ translocating inorganic pyrophosphatase (2), PDR5-like ABC transporter Nucleic acid binding protein, RNA polymerase C, Ribonuclease III, RNA dependent RNA polymerase Lipoxygenase, Chitinase, Catalase, LRR resistance protein Nucellain, Cellulose synthase, Extensin PSI P700 apoprotein, Phosphoribulokinase Cystein protease Envelope protein, α-tubulin 2, Phosphoribosylamine-glycine ligase, Thiamine biosynthetic enzyme, Pol polyprotein, S222, Oxido-reductase, Steroid dehydrogenase, Herbicide safener binding protein, Non-functional folate binding protein, NADH dehydrogenase F subunit, Neuroblastome-amplified protein, Antisense basic fibroblast growth factor, RecF, Sperm tail-specific protein, Pherophorin-S

Nonsense-mediated mRNA decay protein (2), Translation elongation factor eEF-1α(2), eEF2, RNA helicase Serine/threonine protein kinase, Sok1, Calcium dependent protein kinase, Mesotocin receptor Chloroplast membrane-associated protein, Cell wall-plasma membrane linker protein, H+-ATPase, K+ transporter Pyrroline-5-carboxylate synthetase, Tryptophan synthase, Methionine synthase, Asparagine synthetase N-acetylated α-linked acidic dipeptidase, Ubiquitin-specific protease Ascorbate peroxidase Ribosome-sedimenting protein, Acetolactate synthase, Galectin-3, Histidine rich glycoprotein, Gag-pol protein, GP900, Plastid fusion/translocation factor, Nodulin-like protein, Nuclear antigen

CDPK can enhance tolerances toward salt, drought and cold stresses [30]. Upregulation of peroxisomal ascorbate peroxidase indicated increasing in activity for scavenging of reactive oxygen species (ROS) generated under salt stress. Some components of amino acid biosynthesis, such as proline, tryptophan, methionine and asparagine, are up-regulated under long-term salt stress. Expression of RNA metabolism/maturation genes encoding RNA helicase, ribonuclease III, RNAdependent RNA polymerase, nonsense-mediated mRNA decay and translation elongation factors are induced in leaves, in addition to translation initiation factor,



RNase L inhibitor and splicing factor in roots. This indicated that activity of mRNA metabolism/ maturation might be increased to adapt to salt stress. 3. FUNCTIONAL ANALYSIS OF SALT-INDUCIBLE CANDIDATES 3.1. Peroxisomal ascorbate peroxidase (pAPX) Production of ROS is also triggered by secondary effect of salt stress and excessive ROS affects plant productivity. To eliminate ROS, plants have the ROS-scavenging enzymes, such as ascorbate peroxidase (APX), superoxide dismutase, catalase, glutathione reductase, etc. Especially, APX is the ubiquitous ROS-scavenging enzyme, localized in cytosol, stroma and thylakoid membrane in chloroplast, mitochondria and peroxisome. APX catalyzes the reaction, ascorbate and H2O2 to monodehydroascorbate and H2O. Many reports described the importance of APX as a ROS scavenger under oxidative stress. Recently, it was reported that the Arabidopsis mutant lacking cytosolic APX isoform showed growth suppression during normal development, and APX has multiple functions in plants [31]. However, the present fragmentary information can not still established the integrative insight which isoform could play a critical role under each situation. We have obtained the cDNA encoding peroxisomal APX (HvAPX1) in saltstressed barley by differential display [28]. Plant peroxisomal (glyoxysomal) APX is characterized from Arabidopsis, cotton and spinach, but information of its function under environmental stress is still limited. Expression of HvAPX1 mRNA is induced by not only salt, but also heat stress [32]. Overexpression of HvAPX1 in Arabidopsis leads to enhanced tolerance toward heat stress rather than salt stress, suggesting that HvAPX1 would play important roles to scavenge H2O2 generated by heat stress on peroxisomal membrane. Why can overexpressing HvAPX1 enhance heat tolerance in Arabidopsis? Under heat stress, heat responsive gene expression is rapidly modified through the function of heat shock element (HSE). Expression level of Arabidopsis pAPX is not quickly increased under heat stress, due to lacking functional HSE in promoter regions [33]. Hence, HvAPX1 would be effectively acting in Arabidopsis under heat stress, although it is little known about the mechanism of H2O2 production in peroxisome under heat stress. Since acquisition of heat tolerance by HvAPX1 is observed during both vegetative and reproductive stages in Arabidopsis and rice (unpublished data), the common scavenging system might be useful in broad plant species. 3.2. Proline transporter Proline is one of the well-known osmoprotectants, and it is accumulated in many plant species under various stress conditions [34]. Transgenic approaches revealed that proline accumulation leads to enhanced stress tolerance [16]. However, its overaccumulation causes abnormal development in yeast and plant [35]. Therefore, it is considered that proline concentration should be properly regulated according to



environmental condition. Proline is taken into the cells through transporter proteins, such as proline transporter (high affinity) or amino acid transporter (low affinity). We have characterized salt-inducible proline transporter (HvProT) from barley roots [3]. By the assay of yeast mutant lacking proline permease (put4), substrate specificity of HvProT was determined and HvProT is a proline specific transporter (Km = 25.1 µM) unlike betaine/proline transporter in Arabidopsis or tomato. HvProT mRNA is strongly induced in roots by salt stress, and its induction is earlier than that of P5CS, the limiting step of proline synthesis. Under salt stress, HvProT transcript is abundant in root tip region, especially root cap and cortex cells. These results suggested that proline might be transported into root tip cells in barley under salt stress. In tomato pollen, it seems that proline accumulation is accomplished by tomato ProT, but not de novo synthesis of proline by P5CS [36]. Therefore, transportation and tissue-specific accumulation might contribute to stress tolerance. Unexpectedly, growth suppression was observed by overexpression of HvProT gene in Arabidopsis (35S-ProT plant), particularly in aerial tissues [23]. Since growth suppression in 35S-ProT plants is recovered by exogenous addition of proline in the medium, it could be due to deficiency of endogenous proline. On the other hand, 35S-ProT plants were more tolerant than wild type plants toward salt stress, and 35S-ProT plants can grow on MS medium containing 125 mM NaCl. Under non stress condition, proline content is increased in roots, and decreased in shoot of 35S-ProT plants. This indicated that endogenous proline homeostasis is disturbed by overexpressing HvProT. 3.3. Methionine synthase Methionine is one of the essential amino acids in all organisms and synthesized by methionine synthase. Methionine and its derivatives have important roles as substrates in metabolic cycle of one-carbon, donor of methyl group and syntheses of betaine and polyamine, and these functions are crucial for not only stress tolerance, but also normal development. Plant methionine synthase gene is cloned from Arabidopsis, ice plant and maize, but its function is still limited under stress condition. Barley methionine synthase (HvMS) is identified by differential display under salt stress [37]. Yeast mutant lacking methionine synthase showed saltsensitive phenotype, and it was restored to the same extent of wild type strain by overexpressing HvMS. This suggested that methionine synthase is functionally conserved in yeast and plant. Expression of HvMS is induced by various stress treatment, such as salt, drought, cold, ABA and H2O2, although it is controlled by circadian rhythm. Important finding is that amount of HvMS protein is increased by salt stress, but not in rice (as described below). In potato, diurnal changes in transcript amount of methionine synthase do not have influence on protein amount [38]. With posttranscriptional regulation of methionine synthase, genetic engineering of increasing capacity of methionine synthesis is the subject in future.



3.4. Plasma membrane protein 3 The gene encoding plasma membrane protein 3 (AcPMP3) is obtained by differential display from a stress tolerant wild plant, sheep grass (Aneurolepidium chinense (Trin.) kitag). Expression of AcPMP3 gene is induced by salt, drought, ABA, cold, H2O2 and salicylic acid [39]. Barley also has PMP3-like genes and its expression is strongly induced by salt and osmotic stress treatments [40, 41]. It was reported that PMP3 deletion confers sensitivity to cytotoxic cations, including NaCl and hygromycin B. To examine the function of AcPMP3 genes, complementation test was carried out with yeast mutant (∆pmp3, ∆nha1, ∆pmr2) lacking Na+/H+ antiporter and Na+-ATPase that shows more sensitive to salt stress than ∆pmp3 single mutant. It was proposed that loss of PMP3 protein causes membrane hyperporalization, and activates Na+ influx system [42]. Under the control of strong promoter, AcPMP3 gene functionally substituted for deletion of pmp3 in yeast. Furthermore, to determine the physiological roles of PMP3 in higher plants, the effect of knockout mutations in RCI2A, hom*ologous to PMP3, on Na+ uptake and salt tolerance was investigated at both the cellular and whole plant levels in Arabidopsis plants [43]. Although the growth of RCI2A mutants was comparable with that of wild type under normal conditions, high NaCl treatment caused increased accumulation of Na+ and more reduction of the growth of roots and shoots of RCI2A mutants than that of wild type. AcPMP3 protein is a small hydrophobic peptides and it consists of 54 amino acids. Hence, it does not seem to be a transporter protein. In sheep grass, transcript for AcPMP3 gene was observed in root cap and epidermis cells. These facts suggested that PMP3 plays a role directly or indirectly for avoiding over-accumulation of excess Na+ ion in such outer cells of roots, and contributes to plant salt tolerance. 4. COMPARATIVE EXPRESSION ANALYSES OF BARLEY AND RICE DURING THE INITIAL PHASE OF SALT STRESS BY CDNA MICROARRAY cDNA microarray is the advanced tool for comprehensive transcriptome analysis and it enables to monitor expression profile of more than several thousand cDNAs at once. Hence, it is effective to identify genome-wide gene expression, targets for a transcription factor/regulator or crosstalk of signal transduction [44]. Many researches have reported on transcriptome analysis of model plants, such as Arabidopsis and rice, using cDNA microarray [45,46]. In comparison to the established bio-resource in model plants, that of another crops, such as barley, wheat, corn, etc., is just partly available. Therefore, reports on comprehensive expression analysis are still limited using such plants. We have prepared cDNA microarray system using barley salt-responsive genes and investigated barley transcriptome under salt stress. Furthermore, we have attempted to analyze rice transcriptome with barley cDNA microarray. Nucleotide sequences are highly conserved in barley and rice [47], and it would allow heterologous hybridization. Comparative expression analysis demonstrated the differences in early responses to salt stress at molecular level.



The concept of cDNA microarray is based on DNA dot blot analysis. In both dot blot and microarray analyses, probe cDNAs are spotted onto the supporting apparatus, nylon membrane or glass slide. Target cDNAs are transcribed from total RNA or mRNA with 32P, 33P or fluorescent dye (Cy3/ Cy5), and then hybridized with probes. Sometimes complexity of hybridization status raises the background and false signals due to cross-hybridization of family gene and non-specific hybridization. On the other hand, heterologous microarray analysis is also useful for closely related two species [48]. In this case, optimized experimental condition should be determined to increase hybridization efficiency because it is usually lower than that of hom*ologous hybridization. In comparison to dot blot analysis, one of the advantages of cDNA microarray is to enable monitoring large-scale gene expression (more than several thousands) at a time. Microarray experiment needs a series of expensive system, such as DNA arrayer and fluorescent image scanner, and it is still disputable to get repetitive results or normalize array data. Nevertheless, the researches using microarray system are increasing in recent years, suggesting that cDNA microarray is the powerful and effective tool for large-scale expression analysis. 4.1. Early salt-responsive genes in barley and rice roots Ranscriptome analyses were examined at 1 h and 24 h after 200 mM for barley or 150 mM NaCl stress for rice, respectively (Fig. 1) [41]. In barley roots, 13 and 43 genes were significantly up-regulated at 1 h and 24 h, respectively. Of these, the genes encoding tryptophan synthase, PMP3, hypothetical protein, non-functional folate binding protein, cytochrome P450, methionine synthase and no hom*olog, are up-regulated at both 1 h and 24 h. The transcript amount of typical stress-responsive genes, such as proline rich protein (PRP), P5CS, aldehyde dehydrogenase and inorganic pyrophosphatase, are increased at 24 h. Especially, transcript amounts of PMP3, cytochrome P450 and PRP under salt stress are highly increased to 5.3, 19.4 and 17.6 times in comparison to those under control condition. On the other hand, it was observed that expression of only 5 genes was induced in rice roots. PMP3 and inorganic pyrophosphatase, the genes related to maintaining ion homeostasis, are commonly up-regulated in both barley and rice roots, but these inductions were not sustained in rice at 24 h. In yeast, it was shown that loss of PMP3 gene causes saltsensitive phenotype [42]. This indicates that adaptive mechanisms for regulating ion homeostasis are partly conserved in the two species, but it seems that rice can not sustain cellular ion homeostasis for a long time like barley. In roots, similar number of the genes was down-regulated in barley (14 genes) and rice (13 genes). Some genes, such as oxalate oxidase and phosphogluconate dehydrogenase, were down-regulated in both plants. Interestingly, expression levels of both plasma membrane water channel 1 and 2 were rapidly decreased in barley. Under drought stress, overexpression of water channel protein in tobacco causes detrimental effects [49], and it would be due to enhanced symplastic water permeability. Therefore, early down-regulation of water channels might contribute to protection from sudden dehydration. Another difference is that, in contrast to



barley, suppression of tryptophan synthase and methionine synthase was observed in rice roots during the initial phase of salt stress.

Figure 1. Comparative expression analysis in barley and rice under salt stress. Transcriptome was examined at 1 h and 24 h of 200 mM NaCl stress for barley and 150 mM NaCl stress for rice.

4.2. Early salt-responsive genes in barley and rice leaves The number of up-regulated genes in salt-stressed leaves is also lesser in rice than in barley. Only PMP3 gene was up-regulated in rice leaves at 1 h, but its induction was not sustained at 24 h. In contrast, 15 and 11 genes were up-regulated at 1 h and 24 h



in barley under salt stress. These genes are including CDPK, PIP5K, PDR5-like ABC transporter, BADH2, asparagine synthetase, P5CS, methionine synthase, PMP3 and lipoxygenase. On the other hand, 21 and 32 genes were down-regulated in barley and rice, respectively. It was found that the transcripts for glyceraldehyde3-phosphate dehydrogenase (GAPDH), Fd-glutamate synthase, ATP synthase, DnaK like protein and Ribosomal protein L32 were decreased in both plants. Furthermore, down-regulation of transketolase, fructose-1,6-bisphosphatase, phosphoethanolamino-N-methyltransferase, S-adenosyl-methionine-sterol-C-methyltransferase and Rubisco, is observed in rice leaves. As seen in the root transcriptome, methionine synthase and tryptophan synthase were down-regulated in only rice leaves, but not in barley. To confirm the difference in transcriptome between barley and rice, western blot analysis of methionine synthase protein was carried out [41]. Obvious increasing of methionine synthase protein was detected in barley, but not in rice. In barley, various stresses and treatments, such as heat, drought and hydrogen peroxide, triggered expression of methionine synthase mRNA. Although contribution of methionine synthase to stress tolerance is not clear in plants, inducible feature of both mRNA and protein levels in barley is markedly under stress conditions, unlike in rice. 4.3. Divergent responses in barley and rice under salt stress Comparative transcriptome analyses reveal that expression of a different set of the genes is regulated in barley and rice under salt stress. In our research, generally, the number of up-regulated genes is larger in barley and down-regulated genes are larger in rice. One reason is this difference in response to salt stress might be due to the evolutional variation in cis- or trans-acting element of such genes. Also, barley and rice show different physiological responses under salt stress. Two obvious differences in physiological responses were observed during the early phase of salt stress. Leaf water potential was decreased in both plants under salt stress. However, it recovered in barley after 24 h of salt stress, but not in rice. This might be partly explained by expression profiles of the genes involving in osmotic adjustment. Early down-regulation of water channel 1 and 2 genes in barley would contribute to decreasing water permeability across plasma membrane. Transgenic tobacco plants overexpressing plasma membrane-localized water channel showed more sensitive toward drought stress, and this indicated that increment in water permeability is unfavorable trait under water deficit condition. Up-regulation of osmoprotectant syntheses (betaine and proline) is induced in barley. Combined regulation of osmotic adjustment should differentiate the degree of salt tolerance in the two plants. The other finding is tissue-specific pattern of sodium accumulation under salt stress. In barley, sodium content is higher in roots than in leaves. Contrastive pattern is observed in rice. Our comparative microarray analysis does not provide clear frame to explain it although expression manner of inorganic pyrophosphatase and PMP3 genes is different in barley and rice. Some genes involved in photorespiration and glycolysis, are down-regulated in both plants, but the genes encoding amino acid biosynthetic enzyme (proline, methionine, tryptophan, asparagine, serine) are



up-regulated in barley. They seem to reconstitute metabolic balance to adapt to stress condition. We demonstrated the different response in barley and rice using barley cDNA microarray. This array carries barley salt-responsive genes, and it is useful to examine comparative expression analysis between barley and other close species. Genome project is still running for barley and microarray analysis covering the whole cDNAs will make the clear map of expression profilings. Then, it will contribute to endue unique traits to rice. Finally we would like to mention brieflyabout glycinebetaine synthesis in monocotyledonous plants. It was reported that glycinebetaine synthesis occurs in chloroplasts in chenopods, since choline monooxygenase(CMO) and BADH are found to be localized in the chloroplasts [50]. However, localization of glycinebetaine synthesis is totally unknown in other dicotyledonous plants and monocotyledonous plants. We have been characterizing BADHs in Gramineae plants, since BADH catalyzes the last step of glycinebetaine synthesis and it must determine localization of glycinebetaine synthesis. We purified the enzyme from salt-stressed barley leaves. We have found that the major BADH does not have any signal peptide targeting to organelle, i.e. amino acid sequence of N-terminal of the major BADH is consistent with that of the deduced amino acid sequence from BADH2 cDNA [51]. Furthermore, CMO is still mysteriously unknown in monocotyledonous plants. ACKNOWLEDGEMENTS We thank Christine Ehret for critical reading of the manuscript. Research at the author’s laboratory has been supported by the United State Department of Agriculture-National Research Initiatives (Grant #2004-02111) (to L.X) and Bundesministerium fur Wirtschaftliche Zusammenarbeit und Entwicklung (BMZ), the Japanese Ministry of Foreign Affairs (MOFA) (to M.I).

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HISASHI KOIWA Department of Horticultural Sciences, Texas A&M University, College Station, TX77843-2133

Abstract. Acclimation of plants to various environmental stresses involves activation of various signal transduction cascades that activate the expression of genes encoding stress tolerancedeterminants. The established paradigm of this regulation is that the environmental signals are perceived by sensor molecules that trigger cellular stress signaling pathway regulating stressspecific transcription factors. However, number of recent studies in higher eukaryotic system indicated the downstream regulatory steps. Co-transcriptional regulation of RNA polymerase II (RNAPII) complex controls activity of RNAP II during transcription elongation. C-terminal domain of RNAPII largest subunit is a focal regulatory target containing heptad repeats that are reversibly phosphorylated by various kinases and phosphatases. The regulation of plant gene expression at the level of transcription elongation has recently been implied because of the CTDphosphatase family mutants in Arabidopsis that alters stress inducible gene expression. The functional analysis of this gene family started to reveal common and unique mechanisms of plant gene expression among eukaryotes.

1. INTRODUCTION The concerted function of transcription factors is essential in the regulation of gene suites (i.e., transcriptome) that encode determinants of multigene processes like plant growth and development, biosynthesis of complex secondary products, and responses to abiotic and biotic stresses [1-5]. In these processes, developmental programs or environmental stimuli activate “master-switch” transcription factors that control the output of the pathway. However, a cascade output is controlled by a composite series of positive and negative control points that ‘finely tunes’ the signature of the signal. Recent evidence indicates that a high level of gene expression control is imposed during message production or translation [6, 7]. These represent control points that modulate gene expression after the stimulus-induced promoter activation by transcription factors or alter the steady-state gene expression. Substantial information is available about global gene expression regulation that is due to the translational control [6]. Gene regulation at the level of transcript initiation and elongation is an emerging topic in biology [8-11]. Proteins with similar function in the transcription elongation complex mediate substantially 47 Ashwani K. Rai and Teruhiro Takabe (eds.), Abiotic Stress Tolerance in Plants, 47-57. © 2006 Springer. Printed in the Nertherlands.



different human diseases [10]. Such phenotypic differences likely are mediated by the preferential elongation of specific transcripts, however, with the exception of a few notable examples in animals, confirmatory comprehensive data have not yet been reported [12]. Furthermore, although positive and negative regulators of transcription elongation have been identified in yeast and animals, little is known about their identities and functions in plants. In this chapter, we will overview the current understanding of transcriptional regulation by phosphorylation of RNA polymerase II (RNAP II) C-terminal domain and their potential involvement in plant stress response. 2. CTD PHOSPHORYLATION IN TRANSCRIPTION INITIATION AND ELONGATION Eukaryotic mRNA synthesis is catalyzed by RNAP II in a series of processes designated as pre-initiation, initiation, elongation, and termination [13] (Fig. 1).

Figure 1. Phosphorylation and dephosphorylation of RNA polymerase II during transcription cycle. At initiation phase, dephosphorylated, free RNAP II is incorporated into initiation complex assembled at promoter region of a gene. The incorporated RNAP II is then phosphorylated by CDK7/Kin28 (TFIIH subunit) at CTD Ser5. During initiation, CTD Ser5 is predominantly phosphorylated, and this recruits mRNA capping enzyme. CDK9 phosphorylates CTD Ser2 and promotes transition from early elongation to productive elongation phase. During productive elongation phase, CTD is predominantly phosphorylated at Ser2. At termination phase, CTD will be dephosphorylated and RNAP II will be dissociated from the template DNA and recycled. CTD phosphorylation of free RNAP II inhibits RNAP II to be incorporated to initiation complex.

During the transcription elongation step, RNAP II extends a nascent transcript to produce a full-length transcript. This step is often coupled to mRNA maturation processes such as capping, splicing, and polyadenylation [8, 14]. The factors that modulate transcription elongation alter the chromatin structure or target RNAP II in order to affect the pausing/arrest or the continuation of the transcription [15]. The carboxy-terminal domain (CTD) of the largest RNAP II subunit is the key regulatory



target [14]. The CTD contains heptapeptide repeat sequence (YSPTSPS), in which Ser residues at the second and the fifth positions are targets of CTD kinases and phosphatases [16]. The CTD repeats are found only in RNAP II and not in closely related RNAP I and III. Both the number of CTD repeat and non-repeat region of CTD contribute to normal function of RNAP II complex. Phosphorylation status of CTD determines two major forms of RNAP II. The CTD of RNAP IIO is hyperphosphorylated and exhibits lower mobility in SDS-PAGE gels, whereas the CTD of RNAP IIA is hypophosphorylated and exhibit higher mobility than RNAP IIO. Several intermediate form of animal RNAP II include RNAP IIm, which appears when animal cells were exposed to osmotic stress, and RNAP IIe in embryonic cells. The differential phosphorylation that occurs during the transcription cycle determines the functionality of RNAP II and controls the specific interaction between RNAP II CTD and various RNA processing factors. 3. CTD-KINASES Several CTD kinases with different function have been identified in yeast and metazoans (Fig. 1, Table I). Currently, most of them belong to a cyclin-dependent kinase family and have a regulatory cyclin subunit. Phosphorylation of the CTD of the free RNAP II by Srb10 inhibits its recruitment to the preinitiation complex [17]. However, at promoters, Ser5 in the CTD repeats is phosphorylated by TFIIH and is most strongly phosphorylated at the initiation and the early elongation stage [18]. The CTD phosphorylated at Ser5 facilitates recruitment and activation of the capping enzyme [19]. The phosphorylation of Ser2 by PTEF-b orthologs that occurs in the early elongation complex stimulates the transcription elongation [18]. Ser2 of CTD remains phosphorylated during transcription elongation. CTD kinases often play a critical role in specific transcription regulation, such as, for example, transcription of HIV genome [20-22], MIHCII (major histocompatibility complex class II) [23], and heat shock induction of HSP70 (heat shock protein 70) [12]. Table I. CTD-kinase family proteins in human, Saccharomyces cerevisiae. Human TFIIH (CDK7/Cyclin H) PTEF-b (CDK9/Cyclin T)

S. cerevisiae Kin28/

Specificity and function Ser5 phosphorylation at promoter

BurI/BurII Ctk1/Ctk2

CDK8/Cyclin C



Phosphorylate Ser2. Promote transition from early elongation complex to productive elongation complex Ser5 phosphorylation of free RNAP II and inhibit recruitment to the promoter unknown


Ser5 phosphorylation upon heat shock, osmotic stress, and in embryonic tissue



The current understanding of how specific dephosphorylation of the CTD controls these processes is still rudimentary (Fig. 1). FCP1 (TFIIF interacting CTD phosphatase) and SCP1 (small CTD-phosphatase) orthologs represent two classes of known CTD phosphatases that have been characterized in the non-plant systems. FCP1 orthologs and SCPs dephosphorylate Ser2 and Ser5 of the CTD, but FCP1 preferentially phosphorylates Ser2 whereas SCP1 is more biased toward Ser5 of the CTD as its substrate [24-27]. FCP1 promotes elongation activity of the ternary RNAP II complex [28], and recycling of RNAP II [26, 29]. Inactivation of yeast temperature-sensitive FCP1 resulted in overall decline of mRNA synthesis [30]. On the other hand, human FCP1 negatively regulate the transcription of the HIV-1 genome [31, 32] and heat shock gene (hsp70) expression [33]. SCP1 is a negative regulator of the transcription [27]. Interestingly, inactivation of SCP1 in vivo did not affect the transcription of the constitutively expressed genes, but activated the transcription of various inducible promoters such as the dexamethasone-stimulated glucocorticoid receptor activity on the GRE-TK-LUC reporter gene [27]. Functionality of CTD phosphatases is regulated by multiple protein-protein interactions. The activation of FCP1 by RAP74 subunit of the TFIIF complex are essential for FCP1 to dephosphorylate the RNAP II CTD [34-36]. TFIIF is an integral component of the transcription preinitiation complex and the transcribing RNAP II [37-41]. A direct interaction between FCP1 and Rbp4 subunit of the RNAP II has been reported as well [42]. 5. MULTIPLE CTD-PHOSPHATASE-LIKE GENES IN ARABIDOPSIS THALIANA Several genes in the Arabidopsis genome encode polypeptides hom*ologous to the known CTD phosphatases (Table 2, Fig. 2). Based on the presence of distinct domains, they can be categorized into three groups (CPL: CTD phosphatase-like).

Figure 2. CTD phosphatase family proteins have different domain organization. Indicated are representative Arabidopsis (At), Saccharomyces cerevisiae (Sc) and Human (Hs) CTD phosphatase families.



Table 2. CTD phosphatase gene family in Arabidopsis thaliana. Name CPL1 CPL2 CPL3 CPL4 SSP1 SSP2 SSP3 SSP4 SSP5 SSP6 SSP7 SSP8** SSP9 SSP10 SSP11 SSP12 SSP13 SSP14 SSP15 SSP16 SSP17

Gene At4g21670 At5g01270 At2g33540 At5g58000 At1g29780 At1g29770 At5g45700 At5g46410 At5g11860 At3g55960 At3g19600-1 At3g19600-2 At3g17550 At2g04930 At2g02290 At5g23470 At5g54210 At1g20320 At3g15330 At1g43600 At1g43610 **Fused ORFs

Group 1 1 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3

Group 1 CPLs (CPL1 and CPL2) have an FCP1-like catalytic domain and dsRNA binding motif(s) (DRM). Group 2 CPLs (CPL3 and CPL4) have an FCP1-like catalytic domain and a BRCT (BRCA1 C-terminal) domain. Group 3 CPLs (SSP1~SSP17) have only a FCP1-like catalytic domain. The BRCT domain in CPL3 and CPL4 makes group 2 CPLs resemble the prototypical FCP1 CTD phosphatases that bind to TFIIF in the RNAP II complex. Group 1 CPLs are the only known examples of peptides containing both DRM and phosphatase domains. hom*ologs of group 1 CPLs are present in rice (GenBank accession # BAB63701), tobacco (EST# 6128f1 at http://mrg.psc.riken.go.jp/strc/BY-2%20EST.htm), and Zinia elegans (EST# Z713f1 at http://mrg.psc.riken.go.jp/PRIDE/index.html) indicating group 1 CPLs are ubiquitous in plants. DRM can function as a dsRNA-binding and/or a protein-protein interaction domain, and could be a target of regulatory RNA molecules and RNA binding proteins, which often play critical roles in transcription [43-46]. CTD kinase activity of PTEF-b is regulated by 7SK snRNA and by HIV tat protein that binds to tar-RNA of HIV genome [45-49]. Also, human negative elongation factor NELF contains RNA binding subunit [44]. By analogy, CPL1 and CPL2 may bind to the elongating nascent mRNAs, regulatory RNAs, or regulatory peptides through their DRMs, and may be incorporated into the transcription elongation complex. The sequence of group 3 CPLs (SSP1-SSP17) resembles SCP1. As SCP1 preferentially dephosphorylates CTD at Ser5 and affect expression of inducible promoters, the presence of relatively large number of SSP family genes in



the Arabidopsis genome implies that promoter-specific regulation by Ser5 phosphorylation of the CTD may be facilitated by the individual SSP isoforms. 6. MUTATIONS IN GROUP 1 AND GROUP 2 CPL GENES (CPL1, CPL2, CPL3) CAUSE UNIQUE PHENOTYPES Insertion and point mutations in CPL1 (cpl1/ fry2) and CPL3 (cpl3) (Fig. 3) were identified through a forward genetic screening for altered regulation of stressinducible RD29a promoter expression after cold, ABA, or NaCl treatment [50, 51]. Interestingly, cpl1/fry2 and cpl3 mutations, which inactivate isoforms of group 1 and group 2 CPLs, exhibit distinct RD29a expression, growth, stress response and developmental phenotypes [50, 51]. In cpl1/fry2 mutant alleles, hyperinduction of RD29a occurs in response to cold-, ABA- or salt-stress. In contrast, in the cpl3-1 mutant, hyperinduction of the RD29a promoter was ABA specific. The cpl1-1 plants grow more vigorously and flower later than wild type, and the growth of fry2-1 was hyper-sensitive to cold and ABA, whereas cpl3-1 plants exhibit a reduced rate of fresh weight gain and early flowering. We also identified cpl2 mutants using a reverse genetic strategy (Fig. 3). Preliminary reciprocal cross analysis between fry21 and fry2-1/+ cpl2-2/+ plants indicated that CPL2 and CPL1 are partially redundant, as fry2-1 cpl2-2 male but not female double mutant gamete exhibited synthetic lethality (Koiwa et al., submitted). Analysis of cpl2 single mutants is in progress. Apparently, CPLs have both unique and overlapping regulatory functions, perhaps through differential regulation of distinct and common gene sets.

Figure 3. Alleles of cpl mutations identified in this project. Exons (■) were deduced from the cDNA sequence corresponding to CPLs. The open boxes represent untranslated regions. fry21 mutation is a single base substitution whereas the rest are T-DNA insertion mutations.



7. ARABIDOPSIS CPL1 AND CPL2 ARE SER5-SPECIFIC CTD PHOSPHATASES In order to determine the CTD phosphatase activity of CPLs, a recombinant protein for each isoform was expressed in E. coli and purified by Ni2+ affinity column. These fractions exhibited phosphatase activity toward p-nitrophenylphosphate (pNPP) substrate with a pH optimum between 5.5-6.0. CTD phosphatase activity of CPL1 and CPL2 was demonstrated using CTD phosphopeptides composed of 4 tandem repeats of the YSPTSPS sequence phosphorylated at Ser2 or Ser5 of each repeat [24]. Incubation of CTD Ser5-PO4 but not CTD Ser2-PO4 with CPL1 or CPL2 resulted in dephosphorylation of CTD (Koiwa et al, submitted). The Ser5 CTDphosphatase activity of CPL1 and CPL2 had an acidic pH optimum and required specific divalent cations such as Mg2+, Mn2+, Co2+ but not Ca2+, Zn2+, or Cu2+. No detectable activity was observed with similarly purified NusA protein in any of the above assays. The functionally null fry2-1 allele of CPL1 encodes the N-terminal 676-amino-acid CPL1 fragment and lacks the C-terminal 292 amino acid containing the DRMs. In order to test the importance of the DRM in catalytic function of CPL1, a series of CPL1 truncation variant proteins were tested for CTD phosphatase activity. The CPL1 variants, whose C-terminus was shortened up to 467 amino acids, still retained a detectable Ser5-specific CTD phosphatase activity, indicating the DRMs are not essential for its catalytic function. These results established that the group1 CPLs are unique, highly specific CTD Ser5 phosphatases, and implied an essential, non-catalytic function of DRMs in CPL1. 8. CPL3 AND CPL4 ARE FUNCTIONAL PHOSPHATASES THAT INTERACT WITH THE RAP74 SUBUNIT OF TFIIF Phosphatase activity of recombinant CPL3 has been shown using CDP-star as a chemiluminescent substrate [50]. The cDNA encoding CPL4 was isolated using RTPCR and was subcloned into pET44a to produce recombinant NusA-CPL4 fusion protein. Activity of the affinity-purified CPL4 toward pNPP was significantly lower than that of CPL1 and CPL2, requiring longer incubation time. NusA-CPL4 fusion protein did not dephosphorylate any CTD-PO4 (Koiwa et al., unpublished). Similar results were obtained with NusA-CPL3. The low activity toward synthetic substrates and lack of activity toward CTD-PO4 substrate observed with CPL3 and CPL4 are similar to the results with human and S. cerevisiae FCP1 [25, 30, 34, 35]. It appears that the group 2 CPLs require the native RNAP II holoenzyme as their substrate like known human and yeast FCP1 orthologs. Another characteristic of FCP1 orthologs is the interaction with RAP74 (TFIIF large subunit), which likely provides a docking site for FCP1 to associate with the RNAP II holoenzyme. One RAP74 hom*olog was identified in the Arabidopsis genome (AtRAP74: At4g12610). The C-terminal interaction domain of AtRAP74 is hom*ologous to both human and Drosophila RAP74s. When expressed as in vitro-translated peptides, the BRCT domain of both CPL3 and CPL4 interacted with GST-RAP74 fusion protein but not with GST by itself. It appears that CPL3 and CPL4 function as CTD phosphatases in similar



manner to human and S. cerevisiae FCP1, and provided a basis for further biochemical characterization of the group 2 CPLs. 9. CPL1, 3, 4 AND ATRAP74 BUT NOT CPL2 LOCALIZE EXCLUSIVELY IN ARABIDOPSIS NUCLEI, AND THE CPL1 C-TERMINAL REGION IS SUFFICIENT FOR THE NUCLEAR LOCALIZATION To further confirm that CPLs function as nuclear transcriptional regulators, subcellular localization of CPL1, 2, 3, 4 and the Arabidopsis RAP74 hom*olog were determined. The cDNA fragments encoding these proteins were fused to the Cterminus of TAP-GFP-tag [52, 53]. The expression of the fusion protein was driven by a constitutive synthetic promoter [54]. These plasmids were introduced into Arabidopsis protoplasts by a polyethylene glycol (PEG) mediated transformation [55]. All proteins but CPL2 localized exclusively in the nuclei, which were labeled simultaneously by DsRed protein fused to a nuclear localization signal from SV40 T-antigen (NLSSV40:DsRed). The further subcellular localization analysis of truncated CPL1 fragments indicated that the C-terminal 327-amino-acids fragment of CPL1 (CPL1(640-967)) was sufficient for the nuclear localization of the fusion protein (Koiwa et al., submitted). These results supported the hypothesis that CPL gene families function as nuclear transcriptional regulators. 10. FUTURE PERSPECTIVES The recent identification of Arabidopsis CTD phosphatases, as regulators of stressinducible transcription indicated that plant gene expression during stress responses is modulated at the level of RNAP II CTD phosphorylation. CPL1 and CPL2 are novel class of CTD phosphatases containing DRMs. This implicates that RNA molecules may control dephosphorylation of RNAP II transcribing a specific gene or a specific suite of genes. Several mutants that exhibit aberrant osmotic stress and ABA responses are due to the defects of RNA metabolism proteins, such as Sm protein involved in splicing (SAD1) [56], CAP binding protein (ABH1) [57], HYL1 protein that binds to dsRNA and regulates production of micro RNA in plants. These factors may function coordinately as a part of large transcription complex that regulates the osmotic stress signaling. Indeed, a recent study demonstrated that human FCP1 associates with the snRNP complex that contains Sm protein [58]. Identification of CPL1-interacting proteins is an essential component of future investigation. In addition to 4 CPL proteins, Arabidopsis genome encodes 17 small CTD phosphatase-like (SSP) proteins. The biochemical and in vivo function of SSP are currently unknown. It is tempting to speculate that each SSP specifically regulate the expression of unique suite of genes. The biochemical and mutational analysis of each SSP gene along with further characterization of CPL genes will allow us to assess precise functions of these genes, and expand our understanding of transcription elongation in plants.



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KOH IBA Department of Biology, Faculty of Sciences, Kyushu University, f*ckuoka 812-8581, Japan

Abstract. The biomembrane of plant cells contains a high content of highly unsaturated fatty acids (polyunsaturated fatty acids) referred to as trienoic fatty acids. Although the amount of trienoic fatty acids varies according to the living environment of the plant, plants having a high ability to tolerate low temperatures, such as wheat, increase the amount of trienoic fatty acids to account for more than 80% of all fatty acids contained in the biomembrane when acclimated to low temperatures. On the other hand, some plants that thrive in deserts and other hot, dry regions demonstrate a remarkable decrease in the amount of trienoic fatty acids in high-temperature environments. On the basis of these findings, trienoic fatty acids are considered to be intimately involved in plant temperature tolerance. As reported in this study, we have created plants, using genetic engineering techniques, with an excellent temperature tolerance by inhibiting the activity of ω-3 fatty acid desaturase, an enzyme which synthesizes trienoic fatty acids.

1. INTRODUCTION Climate changes have been predicted for the 21st century that will occur on a global scale as the mean air temperature rises due to increasing concentrations of carbon dioxide and other trace greenhouse-effect gases in the atmosphere [1]. Since agriculture and forestry are industries that are engaged in production through utilization of the natural environment, productivity is highly susceptible to climate changes. Consequently, there are concerns over the effects of climate changes brought about by greenhouse effects. In consideration of these circ*mstances, although considerable research has been conducted to evaluate the effects of global warming on agriculture [2-5], efforts are being made to search for specific and practical approaches to enhancing plant tolerance to high-temperature environments. This report provides an introduction to a novel genetic engineering approach, that we recently developed, for imparting high-temperature tolerance to plants [6,7]. The technique introduced here generates an efficacy that is not transient, but rather persists during plant growth. This efficacy is achieved through the direct control of intrinsic gene expression without introducing bacterial or other extrinsic genes. From these advantages, the techniques described here have the potential to evolve into a practical technology. 61 Ashwani K. Rai and Teruhiro Takabe (eds.), Abiotic Stress Tolerance in Plants, 61-68. © 2006 Springer. Printed in the Netherlands.



2. THE RELATION BETWEEN POLYUNSATURATED FATTY ACIDS AND PLANT LOW-TEMPERATURE TOLERANCE Lipids, which are among the basic constituents of biomembranes, have been a focus of attention since the 1960s as one of the factors affecting temperature sensitivity in plants [8]. For example, the physiochemical characteristics displayed by lipid bilayers at different temperatures differ with the species of the lipid head group or their esterified fatty acids, and the their lipid constituents and fatty acid constituents change depending on the environmental growth temperature [9-11]. There has also been an interest in the relationship of low temperature tolerance to the biosynthesis and rearrangement of biomembranes in response to temperature. Since the late 1980s, a series of mutant strains have been isolated in Arabidopsis with altered fatty acid constituents in their biomembranes, providing a breakthrough in the clarification of the pathways by which the polyunsaturated fatty acids contained in biomembrane lipids are generated [12]. The analysis of these mutant strains has shown that the degree of unsaturation of fatty acids of the biomembrane lipids is related to the low-temperature tolerance of a plant [13,14]. fad5 is a mutant strain deficient in 16:0 fatty acid desaturase localized in chloroplasts, while fad6 is a strain deficient in an enzyme similarly localized in chloroplasts that desaturates 16:1 and 18:1 fatty acids (Fig. 1). In addition, fad2 is a mutant strain deficient in 18:1 fatty acid desaturase localized in the endoplasmic reticulum (Fig. 1). The cellular content of polyunsaturated fatty acids, including trienoic fatty acids, are decreased in these mutant strains. Chlorosis (whitening phenomenon of the leaves) and inhibition of growth are observed in these mutants, but not in the wild type, when they are subjected to low-temperature treatment. These findings indicate that polyunsaturated fatty acids are important for the tolerance of plants to low temperatures. 3. AN OVERVIEW ON STRESS SIGNAL TRANSDUCTION CLONING OF THE ω-3 FATTY ACID DESATURASE GENE In general, trienoic fatty acids are present in the greatest amounts among fatty acids contained in plant membrane lipids. Trienoic fatty acids are polyunsaturated fatty acids that have three double bonds, and their content varies considerably according to the plant species and the living environment. Trienoic fatty acids are formed from dienoic fatty acids (having two double bonds) through the activity of ω-3 fatty acid desaturase. Due to the difficulty of characterization by conventional biochemical methods, the cloning of the ω-3 fatty acid desaturase gene has been performed by genetic techniques, namely by map-based cloning methods, using mutant strains of Arabidopsis [15,16]. ω-3 fatty acid desaturase genes cloned thus far are divided into two types consisting of a type localized in chloroplasts (FAD7 and FAD8) and a type localized in the endoplasmic reticulum (FAD3). The expression of the FAD8 gene is temperature-dependent, and is switched on and off by a difference of as little as a few °C, bordering on 25°C [17].



Figure 1. Biosynthetic pathways of major glyceroglycolipids and phospholipids in leaf cells of Arabidopsis and desaturase-deficient mutants. Interruption of the pathway represents the location of Arabidopsis mutations.

4. TRIENOIC FATTY ACIDS AND PLANT LOW-TEMPERATURE TOLERANCE During the initial cloning of the FAD genes, our objective was to develop a plant exhibiting a high tolerance to low temperatures. Previous reports had suggested that increasing the degree of fatty acid unsaturation in biomembrane lipids was important in developing tolerance for low temperatures. When the two types of genes described above were respectively and forcibly expressed by their insertion into tobacco plants, the content of trienoic fatty acids increased in leaf tissue from the insertion of FAD7, localized to chloroplasts [18], while the trienoic fatty acid content increased in root tissue by insertion of FAD3, which is localized to the endoplasmic reticulum [19]. While no difference was observed in low temperature tolerance between plants carrying FAD3 and wild-type plants [19], low temperature tolerance was observed to be improved in the case of plants carrying FAD7 [18]. This difference, however, was only observed under specific and limited conditions. For example, subjecting a wild-type tocacco plant that thrives at 25°C to low temperature treatment for 7 days at 1°C without going through an acclimation process, and subsequently returning the plant to the original temperature environment,



leads to growth inhibition and chlorosis in young leaves prier to beginning development. This reaction to the exposure to low temperature was not observed in the transgenic tobacco plants carrying FAD7. Although this result suggests that trienoic fatty acids enhance tolerance to low temperatures, the effect may be limited to specific plant tissues or growth processes. 5. TRIENOIC FATTY ACIDS AND PLANT HIGH-TEMPERATURE TOLERANCE Although the increase in trienoic fatty acids did not produce as great an improvement in low-temperature tolerance as was expected, we examined the reverse concept, that a decrease in the trienoic fatty acid content of the biomembrane may increase the high-temperature tolerance of plants. In the study described above, the ω-3 fatty acid desaturase gene was linked to a potent expression promoter, such as the cauliflower mosaic virus 35S promoter, to increase the amount of enzyme produced within the plant. However, trangenic lines were found in which the expression of the intrinsic ω-3 fatty acid desaturase gene was co-suppressed by gene silencing. The correlation between the trienoic fatty acid content of the biomembrane and the ability of the plant to tolerate high temperatures was analyzed using two transgenic tobacco lines, T15 and T23, in which the activity of chloroplast-localized ω-3 fatty acid desaturase was decreased by gene silencing. Although trienoic fatty acids in the chloroplast membrane lipids of these transgenic tobacco lines were held to an extremely low level, the level of dienoic acids increased in a manner corresponding to the amount of decrease of trienoic fatty acids (Table 1). In addition, few changes were detected in the lipid molecular species of biomembranes, other than in the chloroplast membrane. Although there was no difference observed in growth between the transgenic tobacco plant and the wild-type plant over the range of low temperatures to the normal growth temperature, at high temperatures, clear differences in growth occurred. For example, in plants cultivated at 30°C for 45 days after germination, the fresh weight of the aerial parts of the T15, T23, and wild-type plants was 492 ± 81 mg, 445 ± 62 mg, and 399 ± 69 mg (n = 5), respectively. At a higher temperature (36°C), marked differences in the growth of the transgenic tobacco lines and the wild type were seen (Fig. 2A). After cultivating plants at 36°C for 45 days, fresh weight of the aerial parts of the T15 and T23 lines and the wild type was 124 ± 49 mg, 123 ± 23 mg, and 13 ± 6 mg (n = 5), respectively. Since growth of the transgenic lines continued to be uninhibited beyond 45 days at 36°C, the observed improvement in high-temperature tolerance has been suggested to be different from that resulting from the induction of heat shock protein [20].



When the plants were exposed to a considerably higher temperature (47°C), the leaves of the wild type withered within 2 days, and the plant bodies exhibited chlorosis after 3 days that resulted in death (Fig. 2B). In contrast, although the growth of the T15 and T23 plants was suppressed, damage due to high temperature was avoided by the plant body (Fig. 2B), and, when returned to a temperature suitable for growth (25°C), the plants continued to grow. Table 1. Fatty acid composition of individual membrane lipids from leaves of wild-type (WT) and gene-silenced tobacco (T15, T23) plants. The major classes of membrane lipids were isolated from the total lipid extracted from mature leaves, and the fatty acid composition was determined. Each value represents the mean of two independent experiments. Dash (-) indicates trace amounts ( Picea engelmannii > Pseudotsuga menziesii var. menziesii > Thuja plicata > Chamaecyparis nootkatensis > Picea sitchensis > Picea glauca x engelmannii > Abies grandis > Pseudotsuga menziesii var. glauca and > Pinus contorta var. latifolia [90]. REFERENCES 1. Diffey, B.L. (1991) Solar ultraviolet radiation effect on biological systems. Review in Phys. Med. Biol. 36: pp 299-238. 2. Fredrick, J.E. (1990) Trends in atmospheric ozone and ultraviolet radiation: mechanisms and observations for the Northern Hemisphere. Photochem. Photobiol. 51, 757-763. 3. Farman, J.C. Gardiner, B.G. and Shaklin, J.D. (1985) Large losses of total ozone in Antactica reveal seasonal CIOxNOx interaction. Nature 315, 207-210.



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Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan 2 School of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan 3 Correspondence author e-mai: [emailprotected]

Abstract. Oxygen deprivation induced by submergence, flooding and waterlogging is an environmental stress that affects the growth of plants and production of crops. Plants undergo metabolic and morphological changes to avoid or alleviate the stresses arising from low oxygen conditions. One well-known metabolic change is activation of the glycolytic and fermentation pathways, which are important for ATP production under anaerobic conditions. In some plant species, morphological changes include elongation of internodes or petioles, aerenchyma formation and formation of a barrier to radial oxygen loss. Under post-anoxic conditions, plants suffer from injurious substances, reactive oxygen species and acetaldehyde. Plants have various mechanisms for metabolizing these harmful molecules to prevent or alleviate post-anoxic injuries. This paper reviews the current understanding of adaptation and tolerance mechanisms of plants that are activated under low oxygen conditions and following re-aeration.

1. INTRODUCTION Rapid environmental changes subject plants to various abiotic stresses that adversely affect their growth and development. Plants can be deprived of oxygen by winter ice encasem*nt, spring floods and heavy rainfall [1]. For example, in Australia, losses of wheat due to waterlogging amount to about 300 million Australian dollars per year [2]. Because plants are sessile, their ability to respond quickly to stressful environmental conditions such as submergence and waterlogging is crucial for adaptation and survival. Thus, it is important to understand how plants adapt to and survive oxygen deprivation. In this article, we focus on the metabolic and morphological changes that occur in plants under submergence and waterlogging and on how plants recover from post-anoxic injury. 111 Ashwani K. Rai and Teruhiro Takabe (eds.), Abiotic Stress Tolerance in Plants, 111-119. © 2006 Springer. Printed in the Netherlands.



2. METABOLIC CHANGES UNDER SUBMERGENCE AND WATERLOGGING Plants are injured by oxygen deprivation as a result of submergence and waterlogging. This type of injury is referred to as anoxic injury (or hypoxic injury). Anoxic injury and hypoxic injury may be caused by a decrease in ATP production, an accumulation of toxic end products of anaerobic metabolism, and cytoplasmic acidosis during extended anaerobiosis [3]. To alleviate this injury, plants make some metabolic changes. Under anaerobic conditions, ATP production is shifted from oxidative phosphorylation to the less efficient glycolysis and fermentation (Figure 1).


Submergence glucose

glucose Glycolysis pyruvate







pyruvate PDC

TCA cycle

Ethanolic fermentation

NAD+ ethanol ADH

NADH 2ATP Oxidative phosphorylation

Lactic fermentation




Figure 1. Changes in metabolism that occur in plants as a result of submergence. During aerobic conditions (left), ATP is produced efficiently through glycolysis, the TCA cycle and oxidative phosphorylation. Under submerged conditions (right), ATP production mainly depends on glycolysis. Ethanolic and lactic fermentations are activated to provide the NAD+ that is required for glycolysis. Ethanolic fermentation is driven by pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH). Lactic fermentation is driven by lactate dehydrogenase (LDH).

Expressions of genes encoding enzymes in these pathways are induced in response to oxygen deprivation [4]. As NAD+ is needed to sustain glycolysis, fermentation pathways play a role in providing NAD+ to the glycolytic pathway. Three main fermentation pathways, whose end products are ethanol, lactate and alanine, are enhanced during anaerobic conditions [2]. Among the three fermentation pathways, ethanolic and lactic fermentations can regenerate NAD+ from NADH (Figure 1). It has been suggested that cytosolic pH controls the ratio between ethanolic fermentation and lactic fermentation [5,6,7], i.e., a decrease in cytosolic pH increases ethanolic fermentation and decreases lactic fermentation. Lactate, an end product of lactic fermentation, could cause a decrease of cytosolic pH. In addition,



H+-ATPase pumps could be responsible for the decrease of cytosolic pH [8,9]. Because low pH inhibits the activity of lactate dehydrogenase (LDH) and increases the activity of pyruvate decarboxylase (PDC) (Figure 1), the main fermentation pathway shifts from lactic fermentation to ethanolic fermentation [10, 11]. In rice, the anoxia-tolerant cultivars FR13A and Calrose have higher rates of ethanolic fermentation than the anoxia-intolerant cultivars IR22 and IR42 [12,13]. An increase of the rate of ethanolic fermentation in rice leads to a corresponding increase in survival of rice under submerged conditions [14]. By contrast, a rice mutant with reduced ADH activity was more vulnerable to submergence than the wild type of rice [15]. Taken together, these results indicate that ethanolic fermentation plays an important role in the adaptation of plants to low oxygen conditions. 3. MORPHOLOGICAL CHANGES UNDER SUBMERGENCE AND WATERLOGGING In order to avoid hypoxia stress, some plants undergo morphological changes such as (1) elongation of internodes or petioles, (2) aerenchyma formation, and (3) formation of a barrier to radial oxygen loss (ROL). Each of these changes is described below. 3.1. Elongation of internodes or petioles Deepwater rice and Rumex palustris have an ability to elongate their internodes and petioles, respectively, under submerged conditions [16,17]. The elongation of these organs allows the plants to obtain oxygen above the surface of the water. As the diffusion of gas in water is 10,000 times slower than in air, gases (e.g., ethylene) produced in plants cannot be discharged in water [18]. As a result, the amount of ethylene increases in the internodal air spaces of deepwater rice and in the petioles of R. palustris soon after submergence [17,19]. The increased ethylene can generally cause the decrease of abscisic acid (ABA) and the increase of gibberellin (GA), both of which promote the elongation of internodes or petioles. Even under submerged conditions, the synthesis of ethylene is maintained by activation of the expressions of genes for enzymes involved in ethylene biosynthesis, such as ACC synthase and ACC oxidase [16,17]. In plants, ethylene is synthesized from S-adenosyl-Lmethionine (SAM) via two reactions catalyzed by ACC synthase and ACC oxidase [20]. In R. palustris, expressions of RP-ACS1, an ACC synthase gene, and RPACO1, an ACC oxidase gene, are up-regulated under submerged conditions [17,21]. In deepwater rice, the induction of Os-ACS1, Os-ACS5 and Os-ACO1 are observed in the intercalary meristem under submergence [22, 23, 24]. Significant increases in the activities of ACC synthase and ACC oxidase were also observed in deepwater rice and R. palustris under submergence [16,17,21,23]. Other hormones related to elongation during submergence are ABA and GA. Within 1 h of submergence, the ABA level in petioles of R. palustris was reduced by 80% [17] and after 4 h of submergence, the ABA level in deepwater rice was



reduced by 55% [23]. Application of ABA to submerged R. palustris and deepwater rice significantly inhibited their elongation [17,25]. On the other hand, when deepwater rice was treated with ethylene for 3 h, the ABA level in the intercalary meristem and the cell elongation zone decreased by 75% [25]. Ethylene also decreased the level of ABA during elongation of petioles of R. palustris [17]. These results indicate that ethylene is responsible for the decrease of ABA contents in deepwater rice and R. palustris under submerged conditions. Submergence-induced elongation in plants also depends on the endogenous GA level. The level of GA1, which is the active GA in rice, and GA20, which is the immediate precursor of GA1, increased during submergence [25]. Moreover, the inhibition of growth of internodes in deepwater rice by ABA was recovered by GA [25], and ethylene enhanced the responsiveness of deepwater rice internodes to GA [26]. These findings suggest that the rapid growth of deepwater rice internodes is controlled by increased ethylene under submergence, thereby altering the balance between the endogenous levels of ABA and GA [25]. 3.2. Aerenchyma formation The aerenchyma is an internal aeration system for the transfer of oxygen from the shoot that increases plant survival in low-oxygen soil environments. The aerenchyma occurs in two forms, schizogenous aerenchyma and lysigenous aerenchyma [27,28]. Schizogenous aerenchyma occurs when intercellular gas spaces form during tissue development without cell death. Spaces are formed by differential growth, with adjacent cells separating from one another at the middle lamella. Schizogenous aerenchyma formation is often observed in wetland species like Rumex [28]. Lysigenous aerenchyma formation is formed by cell death in root cortex cells and the cell death is first detected in the mid cortex [29] (Figure 2).

Figure 2. Transverse section of maize primary root about 15 mm from the base of the root. A. Root before waterlogging (aerobic conditions). B. Root 96 hours after the initiation of waterlogging, in which aerenchyma formation was observed in the mid cortex. Photographs provided by Ryosuke Watanabe (University of Tokyo).

Ethylene induces lysigenous aerenchyma formation in the roots of maize [30,31]. Hypoxia stimulates ethylene biosynthesis by enhancing of the activities of ACC



synthase and ACC oxidase [32], which indicates that the cell death in the root cortex of maize under low oxygen conditions occurs downstream of ethylene signal transduction. In addition, experiments with some specific inhibitors suggest that heterotrimeric G protein-related signaling, Ca2+ signaling, and protein phosphorylation are involved in the formation of lysigenous aerenchyma [29,33]. 3.3. Formation of a barrier to radial oxygen loss (ROL) Roots of rice and wetland species also contain a barrier to ROL in the basal zones [30,34,35]. This barrier, which is composed of a suberized exodermis and endodermis and a layer of lignified sclerenchymatous cells [36,37], enhances the amount of oxygen diffusing into the root apex and promotes the development of an aerobic rhizosphere around the root tip [38]. Thus, the effectiveness of the aerenchyma can be increased by the formation of a barrier to prevent ROL from roots. 4. ALLEVIATION OF POST-ANOXIC INJURY In addition to being damaged under anaerobic conditions, plants may be damaged during re-aeration following anaerobic conditions. The latter type of damage is known as post-anoxic injury (also referred to as post-hypoxic injury by some authors) [39,40,41]. Post-anoxic injury appears to be caused by acetaldehyde and reactive oxygen species (ROS). Examples of the latter are superoxide radical (O2.-), hydroxyl radical (OH.), and hydrogen peroxide (H2O2). The production of ROS is immediately induced upon exposure of anaerobic plant tissues to normal oxygen tension and, as a result, proteins, nucleic acids and membranes can undergo severe peroxidation [42,43]. Plants have some defense mechanisms for scavenging ROS after re-aeration. Superoxide dismutase, ascorbate peroxidase and catalase (CAT) are mainly engaged in the detoxification of ROS in plants [1,44]. Re-aeration also induces the production of acetaldehyde, as a result of oxidation of ethanol, which is produced and accumulated by ethanolic fermentation under anaerobic conditions [45,46] (Figure 3). Ethanol is assumed to be rapidly oxidized to acetaldehyde by alcohol dehydrogenase (ADH) and/or CAT [39,47,48]. CAT probably oxidizes ethanol through its reduction of H2O2 that is produced during re-aeration [39,47]. Acetaldehyde is harmful to cells because of its tendency to form acetaldehydeprotein and acetaldehyde-DNA adducts [49,50]. Cells possess mechanisms to metabolize acetaldehyde. Aldehyde dehydrogenase (ALDH) catalyzes the conversion of aldehydes to the corresponding acids [51] (Figure 3). Rice has two mitochondrial ALDHs, ALDH2a and ALDH2b [52,53]. The amount of ALDH2a transcripts increased under submerged conditions, whereas the amount of ALDH2b transcripts decreased. Interestingly, re-aerated rice plants showed an intense ALDH2a induction, despite a decline of ALDH2a mRNA. Along with the increase of ALDH2a protein, acetaldehyde-oxidizing ALDH activity increased, thereby causing the acetaldehyde content to decrease in rice during re-aeration [54]. These findings suggest that rice ALDH2a mRNA is accumulated in order to quickly metabolize



acetaldehyde that is produced upon re-aeration, and that mitochondrial ALDH is involved in the alleviation of post-anoxic injury induced by acetaldehyde. In conclusion, plants possess complex mechanisms to avoid and alleviate anoxic and post-anoxic injuries and to tolerate low oxygen conditions in combination with metabolic and morphological changes. Much more research is needed to fully understand the mechanisms for adapting to low oxygen stress in plants because many factors are intricately involved. In addition, it is not known how plants sense low oxygen levels. Further studies involving forward and reverse genetics and highthroughput techniques such as microarray analyses should elucidate the intricate mechanisms involved in adapting to and recovering from low oxygen conditions, as well as provide clues on how to produce crops that can tolerate such conditions.

Figure 3. Proposed metabolic pathways of rice under submerged conditions and following reaeration. Under submerged conditions (left), pyruvate, which is produced by pathways such as glycolysis, is converted to acetaldehyde by PDC. At the same time, acetaldehyde is converted to ethanol by ADH and to acetate by aldehyde dehydrogenase (ALDH). When the submerged plants are transferred to aerobic conditions (right), the anaerobically accumulated ethanol is rapidly oxidized to acetaldehyde by the reverse reaction of ADH and/or the peroxidation of ethanol by catalase (CAT) during the conversion of H2O2 to H2O. Evidence suggests that ALDH efficiently detoxifies the phytotoxic acetaldehyde by the rapid increase of mitochondrial ALDH under re-aeration.

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DANIKA L. LEDUC1 AND NORMAN TERRY Department of Plant Biology, University of California, Berkeley, CA 94720-3102, USA 1 Correspondence author e-mai: [emailprotected]

Abstract. Phytoremediation uses plants and associated microbes to remove, sequester, and detoxify contaminants, particularly trace elements. The great potential of this low-cost, low-management approach has spurred researchers to increase the efficiency of this natural process through the use of genetic engineering. Plants used for phytoremediation face a primary stress emanating from the high local concentrations of contaminants as well as possible secondary stresses such as extreme temperature, salinity, desiccation, flooding, and/or high light. Since the total amount of a contaminant removed is a product of the total biomass of the harvestable tissue and the concentration of the contaminant in those tissues, it is critical that phytoremediating plants tolerate contaminant stress through detoxification mechanisms rather than avoidance or exclusion mechanisms. At the same time, they should survive the sub-optimal growth conditions often associated with contaminated sites. For this reason, the introduced genes often play a role in increasing the stress tolerance of the engineered plants. Successful genetic engineering approaches range from the transfer of genes with specific detoxification function to overexpression of genes involved in ameliorating oxidative stress in general. Advances in related fields, including rapid genome sequencing, microarrays, and more sophisticated gene expression systems, should eventually lead to an increase in the number of engineered plants suitable for field-use.

1. INTRODUCTION Phytoremediation is the use of plants and their associated microbes to remove, sequester, and detoxify contaminants from soil and water [1]. This process occurs naturally in plants. Frequently, contaminants, especially trace elements, are transported into plant roots because of their essentiality or chemical similarity to an essential element. In phytoextraction, the contaminants are further transported from root to shoot where they can be harvested in the above-ground biomass [1]. A subset of contaminants, particularly selenium and mercury, can be metabolized in the plant to volatile (gaseous) forms [1]. This process, referred to as phytovolatilization, is of special interest because it can potentially remove all the contaminant from the local ecosystem. Phytostabilization, the use of plants to contain soil pollutants by preventing erosion, will not be discussed in this review. Phytoremediation is an attractive remediation approach for dealing with wastewater, soils, and sediments contaminated with heavy metals, metalloids, 123 Ashwani K. Rai and Teruhiro Takabe (eds.), Abiotic Stress Tolerance in Plants, 123-133. © 2006 Springer. Printed in the Netherlands.



radionuclides, and organics, such as polyaromatic hydrocarbons and polychlorinated biphenyls [2]. Of particular importance are its low cost and low management requirements [3]. Currently used physicochemical methods are prohibitively expensive, forcing governments to make difficult choices of which sites to remediate [4]. Biopiles of microbes are a low-cost but difficult to manage approach that requires a constant carbon source and seeding to maintain the growth of “useful” microbes compared to that of other microbes that constantly invade the site [5]. In phytoremediation, sunlight provides the energy for plants (through photosynthesis) to generate carbon products to support microbial populations associated with the root system. Thus, phytoremediation offers an attractive alternative because it lessens the need for constant management and for energy inputs [6]. Phytoremediation has been achieved in a number of small-scale field experiments with a variety of native species [e.g. 7-9]. The adoption of phytoremediation for contaminant cleanup has been limited primarily by the inefficiency of natural plant processes. Most plants do not accumulate contaminants, either because they exclude their uptake or because they suffer reduced biomass and growth in the presence of the contaminant. Some plants on the other hand, known as hyperaccumulators, are tolerant of the contaminant (especially toxic trace elements) and may accumulate several thousands of parts per million in their aboveground tissues [10]. However, this high level of accumulation is generally offset by low biomass and slow growth rate, so that the overall efficiency of phytoremediation by hyperaccumulators is not high [11]. Other plants, known as secondary accumulators, are more successful at phytoremediation because they accumulate moderate concentrations of trace element contaminants while maintaining a relatively fast growth rate and high biomass [12,13]. Several attempts have been made to increase the phytoremediation efficiency of secondary accumulators through genetic engineering, an approach that has met with a number of successes [e.g. 14-26]. In our own laboratory for example, we have been able to genetically engineer Indian mustards that were able to outperform wildtype plants in removing selenium from toxic sediments under field conditions [27]. 2. ENHANCING PHYTOREMEDIATION THROUGH GENETIC ENGINEERING In phytoextraction, the total amount of contaminant removed (during one growth cycle) is equal to the concentration of contaminant in the shoot tissue multiplied by shoot biomass [28]. The ultimate goal of phytoextraction is clean up the contaminated soil and water in the shortest possible time, i.e., in as few growth cycles as possible. This may be achieved through genetic engineering. One approach, for example, is to overexpress metal transporters so as to increase the efficiency of uptake of the contaminant into root or shoot tissues [22, 29, 30]. This approach is complicated by the fact that the transgenic plant may not have the ability to detoxify the increased levels of contaminant it has accumulated [30]. Nevertheless, transgenic plants of Arabidopsis thaliana overexpressing YCF1 exhibited increased tolerance and accumulation of lead and cadmium because of increased



transport of these metals to the vacuole [31]. Another approach is to engineer plants to exude organic acids that alter rhizosphere pH so as to increase the solubility and bioavailability and therefore uptake of contaminants [32-34]. The ability of plants for phytoremediation can be greatly improved by increasing tolerance to environmental stresses. This allows the plant to maintain a high biomass and fast growth rate in environments potentially unfavorable for growth. Although the primary stress encountered by the plants is likely to be the toxicant to be remediated, the plant may also have to contend with other stresses, such as moderate to high levels of other contaminants, poor soil quality (pH, mineral deficiencies, etc…), aridity or flooding, and temperature variations [27]. Plants have evolved three general strategies for tolerating high concentrations of trace metal contaminants in soil and water. The first is to avoid the metals all together. This can be accomplished through such means as exuding organic acid chelates through the roots or by changing the pH in the rhizosphere so that trace metals are converted to a less bioavailable form. In several species of plants, for instance, tolerance to high soil concentrations of aluminum is correlated with root exudation of organic acids [35,36]. A second strategy is to trap toxicants in the roots through the over-production of chelating molecules [37]. This strategy is particularly effective for metals that exert their toxicity in the shoots, since they are prevented from being transported to the shoots. Finally, some plants tolerate metals by detoxifying them, either through chelation, sequestration, or metabolism to less toxic forms [3841]. Only this latter strategy is useful for phytoextraction since the metals are accumulated in the easily harvestable plant shoots. 3. LESSONS FROM NATURE: DESIGNING STRESS TOLERANT PLANTS FOR PHYTOREMEDIATION A key step in any genetic engineering project is to identify the appropriate genes to introduce into target plants suitable for phytoremediation. Such a target plant ideally should have a fast-growth rate, high biomass, and moderate tolerance to trace element contaminants and environmental stresses [42]. Examples of plants that have been used for this purpose include tobacco (Nicotiana tabacum), Indian mustard (Brassica juncea), and trees such as poplar (Populus sp.). The selection of genes to be introduced into target plant species may be identified through a variety of techniques. Early hybridization work provided some insight into the genetic basis of tolerance in a variety of species [43,44]. The production and screening of random mutants, particularly with the model plant species, Arabidopsis thaliana, has led to the discovery of a number of genes involved in heavy metal tolerance [45,46]. Under the premise that genes whose expression is modified by the presence of heavy metals are important in the plant’s heavy metal stress response, modern microarrays will likely become more important in identifying such genes. That is because with current genetic engineering technology, we are generally altering the expression of only one or two genes, so we are merely tweaking the plant’s natural abilities. One special advantage of genetic engineering is the ability to transform plants with genes from other species rather than upregulating an already existing plant



stress response. The genomes of hyperaccumulating plant species are of interest to researchers seeking genes for genetic engineering. Hyperaccumulators are able to accumulate trace elements (e.g., Se, As, Pb, Ni, and Zn) to thousands of parts per million in their shoot tissues [40]. Generally, this adaptation is specific to only one element so that its genetic basis is often very specific rather than a general stress response. The problem with hyperaccumulators is that their phytoremediation efficiency is often limited by their slow growth rate and low biomass [11]. In genetic engineering, it is technically easier to transfer genes responsible for hyperaccumulation to fast-growing, high biomass plants than to increase the growth rate of hyperaccumulators themselves. For this reason, hyperaccumulators are currently viewed as gene sources rather than hosts for transformation. Another source of potential genes for genetic engineering is the genomes of extremophile microbes, which have been discovered in a wide range of extreme environments that do not support the life of plants or higher organisms. Their rapid evolution has resulted in microbes that can tolerate such diverse stresses as extreme cold, heat, pH, salinity, and high metal concentrations [47]. In fact, there are microbes that conduct anaerobic respiration of selenium and arsenic [48]. There are, however, several complications with using microbial genes including different codon usage, difficulty in culturing, and the fact that gene regulation in a multicellular organism might be different. 4. GENETIC ENGINEERING STRESS-TOLERANT PLANTS FOR PHYTOREMEDIATION: SUCCESSES Success in genetic engineering stress-tolerant plants has been the culmination of extensive work in identifying critical genes, which, on overexpression increase either tolerance to a specific metal contaminant or general stress tolerance that results in increased plant biomass. An obvious strategy for increasing the tolerance of a plant to a toxic trace element is to increase its ability to convert the trace element to a less toxic form. Typically, such a plant would then be able to accumulate higher levels of this detoxified form. An example of this approach is the overexpression of the gene encoding selenocysteine methyltransferase (SMT) in Indian mustard [25]. The gene encoding this enzyme was first identified in the Se hyperaccumulator, Astragalus bisulcatus, and was determined to be a key component of the hyperaccumulation mechanism [49]. The toxicity of selenium is due in part to its chemical similarity to sulfur. The misincorporation of selenoamino acids analogs of the sulfur-amino acids, cysteine and methionine, into proteins can alter enzyme structure and activity. The role of SMT in hyperaccumulation is to methylate selenocysteine to the non-protein selenoamino acid, methylselenocysteine. Thus, selenium is detoxified by diverting selenium flow away from the selenoamino acids, and therefore, from proteins [50]. Transgenic Indian mustard overexpressing SMT exhibited increased selenium tolerance and accumulation [25]. Another specific detoxification pathway that has been transformed into plants for phytoremediation is the bacterial mer operon [51]. The merA and merB genes



encode mercuric reductase and methylmercury lyase, respectively. Expressed together these enzymes function to convert organic or inorganic mercury to elemental mercury that escapes from the plant in volatile form. A variety of plant species overexpressing merA and merB have increased tolerance and accumulation of both inorganic and organic mercury forms [52]. MerA and merB genes have been introduced into plants using chloroplast transformation (e.g. in tobacco) as well as the more common nuclear transformation approach [53]. Chloroplast transformation, although slightly more complicated, results in greater transgene expression, maternal transfer of transgenes, which restricts gene flow through pollen spread, and may afford a greater protective effect against metals with specific toxicity against the chloroplasts [54]. Specific detoxification mechanisms may be introduced at the same time as increasing expression of genes involved in plant stress response. A striking example of this is seen in the development of Arabidopsis overexpressing both arsC, encoding arsenate reductase, and gshII, the gene encoding γ-glutamylcysteine synthetase (ECS) for increased arsenic resistance [19]. Arsenate is the predominant form of bioavailable arsenic. The first-step in one proposed arsenic detoxification model is the reduction of arsenate to arsenite. Since a plant arsenate reductase gene was not available, the authors used a bacterial gene. Although arsenite is more toxic than arsenate, it has the advantage that it can be detoxified through chelation with thiolcontaining compounds, such as glutathione (GSH) and phytochelatins (PCs). By overexpressing an arsenate reductase in Arabidopsis, the proportion of As present as toxic arsenite increased [19]. Because Arabidopsis would not be able to effectively detoxify this greater pool of arsenite without a concomitant increase in thiolcontaining compounds, the authors overexpressed ECS in the same plants. ECS catalyzes a rate-limiting step in the production of PCs, short Cys-containing peptides known to chelate a variety of metals/metalloids [55]. Heavy metals may express their toxicities through individual symptoms such as stunted growth, root damage, necrosis, etc. However, the mechanism of damage may involve oxidative stress through the production of reactive oxygen species [56]. As such, genes involved in ameliorating oxidative stress may afford protection against a wide variety of trace element contaminants, which is an especially important asset for sites contaminated with multiple metals. In order to genetically engineer Indian mustard for enhanced tolerance and accumulation of heavy metals, transgenic plants overexpressing glutathione synthetase (GS) and γ-glutamylcysteine synthetase (ECS) were developed. GS and ECS are enzymes that catalyze rate-limiting steps in the production of glutathione (GS) and phytochelatins (PC) [16,17]. The role of PCs in cadmium chelation and sequestration has been well established, and, as expected, these plants had enhanced cadmium tolerance and accumulation [16,17,57]. However, these plants have since been shown to tolerate and accumulate a wide variety of heavy metals [21]. Similarly, Indian mustard overexpressing the Arabidopsis gene encoding ATP sulfurylase (APS) was originally developed for Se phytoremediation [15]. APS catalyzes a rate-limiting step in the sulfur/selenium assimilation pathway in plants, and its overexpression results in increased selenate uptake and eventual reduction to selenite [58]. At the same time, though, APS overexpression also increases sulfate



uptake and reduction. Since reduced sulfur forms (such as Cys) are limiting substrates for the synthesis of GSH and PCs, the greater pool of reduced sulfur may allow for protection against heavy metals as well. Indeed, APS Indian mustard plants were more effective than wild type in tolerating and extracting a wide variety of heavy metals from contaminated soil [26]. Recently, Indian mustard lines overexpressing APS, ECS and GS, respectively, were studied in the first successful phytoremediation field trial of transgenic plants in the United States [27]. The plants, along with wild type, were grown on a mix of clean topsoil and high Se-sediment dredged from drainage water canals in central California. The growth conditions on this site were sub-optimal since the levels of soil salinity and extractable B are considered to be detrimental for normal plant growth, especially under the hot and arid climatic conditions commonly present in this part of California [59]. All three lines accumulated significantly higher concentrations of Se in their shoots, up to 430% more in the case of APS, even though the ECS and GS were not specifically thought to have increased Se [57]. The transgenics were at least equally tolerant to these soil and field conditions compared to wild type, despite their higher Se accumulation. Despite their greater accumulation of selenium, the transgenic plants were as, or more, tolerant of the soil and field conditions as the wild type. The GS transgenic line was particularly tolerant of the contaminated soil [57]. GS plants grown on the sediment-soil mixture attained 80% of the biomass of plants of GS plants grown on control soil, indicating that these plants were more tolerant of the high levels of soil Se and sodium, as well as greater tolerance to other adverse growth conditions, such as heat or drought. Since the production of GSH is known to be part of the plant’s protective response to a variety of stresses including salinity stress, chilling, heat shock, pathogen attack, active oxygen species, air pollution, and heavy metals, the better growth of the GS line on contaminated soil could well have been due to an elevated glutathione concentration [60-63]. Besides glutathione, increased levels of metallothioneins (translated heavy-metal binding peptides), superoxide dismutases, other reducing agents, such as ascorbate, and organic acids, such as malate and citrate, have been observed in response to multiple and seemingly diverse stresses such as wounding, pathogen attack, drought, heat, and metal stress [64-67]. This suggests that the overexpression of certain oxidative stress response genes could indeed afford a wide range of protection against the primary (metal contaminant) and secondary (environmental conditions) stresses faced by plants used in phytoremediation. 5. GENETIC ENGINEERING STRESS-TOLERANT PLANTS FOR PHYTOREMEDIATION: COMPLICATIONS There have been a number of successes in the past ten years with respect to using genetic engineering to increase plant tolerance and accumulation of trace element contaminants. However, there is much to learn before genetically engineered plants can be used for large-scale phytoremediation processes. The biggest obstacle currently is public fear of genetically modified organisms. Although the use of



genetically engineered plants for phytoremediation is more acceptable than genetically modified food products, there are legitimate concerns to be addressed. One is that the super-accumulating plants will transport more contaminants from soils and water into the aboveground plant tissues so that contaminants may become more bioavailable to wildlife in the surrounding ecosystem [68]. Of particular concern is the risk to endangered wildlife populations. A whole ecosystem approach, accounting for total concentrations and chemical forms at different trophic levels, may be required to accurately evaluate the overall risks and benefits of phytoremediation in different environments. Certain elements, such as selenium and mercury, can be metabolized to volatile forms, which are released as gases into the atmosphere and, therefore, removed from the local ecosystem. As such, genetic engineering to increase the flux through these metabolic pathways could be an effective means of alleviating risk to the local ecosystem [69,70]. Another concern is the possibility of transgene flow (either the transgene itself or selectable markers) to the ecosystem. Fortunately, researchers have been developing methods to address this concern [70]. Approaches such as chloroplastic engineering and induced sterility will reduce gene flow through pollen [54,71]. At the same time, methods for removing selectable marker genes following hom*ozygous line selection, which typically encode antibiotic resistance, following hom*ozygous line selection have been developed [72]. Researchers involved in genetic engineering plants for phytoremediation also face a number of other technical problems. Perhaps the most critical challenge for the field is to develop plants with truly superior levels of contaminant accumulation that still maintain near-normal biomass. Typically, the transgenic plants produced thus far have a several-fold (i.e., somewhat less than 10-fold) greater accumulation of contaminants than wild type. It is commonly believed that phytoremediation technology will be adopted only when the accumulation approaches 100- or 1000fold more than wild type. If such concentrations are even possible has yet to be determined. It is clear that we have a great deal to learn if this barrier is to be overcome. In particular, we need to improve our ability to predict the effects of gene overexpression, since there are now several examples of overexpression of oxidative response genes that did not result in plants with increased phytoremediation potential [73]. Overexpression of the same gene in different species can even result in different effects, increasing tolerance in one and sensitivity in another [74]. The gathering and analysis of genome, transcriptome, proteome, and metabolome data along with more sophisticated modeling techniques should enhance our ability to predict the effect of transgenes on contaminant uptake and tolerance. Similarly, genetic engineering can have undesired consequences. For instance, peptides and metabolites involved in heavy metal binding frequently play a role in essential-metal homeostasis and transport, and, consequently, plant development [75]. Overexpressing such proteins could lead to chelation and sequestration of essential heavy metals and/or a disruption of normal plant development. More generally, constitutive overexpression of a transgene may tax the plant’s energy and substrate resources. Indeed, transgenic plants are frequently smaller and slower in developing than wild type plants when grown under control conditions. Here again,



more sophisticated expression systems may be needed to overcome these barriers. Examples of these are the use of stress-inducible or tissue-specific promoters that limit the expression of the transgene to the times and tissues when they are needed, allowing the plant to grow and develop normally [76]. 6. FUTURE PROSPECTS Even though the use of genetic engineering for phytoremediation is a very young field of research, it has had a number of important successes. A solid foundation has been laid through the demonstration that specific detoxification mechanisms can be successfully transferred from hyperaccumulators or microbes into plants. At the same time, the ability of general oxidative stress response genes to afford protection against multiple metals and environmental stresses suggests that high-biomass accumulating plants can be developed through genetic engineering. Advances in bioinformatics and the development of more sophisticated expression systems may be used to create efficient, publicly acceptable plants that can be used for wide-scale phytoremediation projects. REFERENCES 1. Terry, N., Zayed, A.M., de Souza, M.P. and Tarun, A.S. (2000) Ann. Rev. Plant Physiol. Plant Mol. Biol. 51, 401-432 2. Suresh, B. and Ravishankar, G.A. (2004) Phytoremediation. a novel and promising approach for environmental clean-up. Crit. Rev. Biotechnol. 24, 97-124. 3. Glass, D.J. (2000) Economic potential of phytoremediation: In Phytoremediation of Toxic Metals – Using Plants to Clean up the Environment (Raskin, I. and Ensley, B.D., eds). New York. 4. Cunningham, S.D. and Berti, W.R. (2000) Phytoextraction and phytostabilization: technical, economic and regulatory considerations of the soil-lead issue: In Phytoremediation of Contaminated Soil and Water (Terry, N. and G. Bañuelos, G., eds). FL : CRC Press LLC, Boca Raton. 5. Cookson, J.T. (1995) Bioremediation Engineering, Design and Application. New York, McGrawHill, Inc. 6. Chaudhry, Q., Blom-Zandstra, M., Gupta, S. and Joner, E.J. (2005) Utilising the synergy between plants and rhizosphere microorganisms to enhance breakdown of organic pollutants in the environment. Environ. Sci. Pollut. Res. Int. 12, 34-48. 7. Blaylock, M. (2000) Field demonstrations of phytoremediation of lead-contaminated soils. In Phytoremediation of Contaminated Soil and Water (Terry, N. and G. Bañuelos, G., eds). FL: CRC Press LLC, Boca Raton. 8. Horne, A.J. (2000) Phytoremediation by constructed wetlands: In Phytoremediation of Contaminated Soil and Water (Terry, N. and G. Bañuelos, G., eds). FL : CRC Press LLC, Boca Raton. 9. Bañuelos, G.S. (2000) Factors influencing field phytoremediation of selenium-laden soil. In Phytoremediation of Contaminated Soil and Water (Terry, N. and G. Bañuelos, G., eds). FL : CRC Press LLC, Boca Raton. 10. Brooks, R.R. (1994) Plants that hyperaccumulate heavy metals. In Plants and the Chemical Elements: Biochemistry, Uptake, Tolerance and Ttoxicity (Garago, M.E., ed). Weinheim, Germany: VCH Verlagsgesellsschaft, pp. 88-105. 11. Cunningham, S., Shann, J., Crowley, D. and Anderson, T. (1997) Phytoremediation of contaminated water and soil: In Phytoremediation of Soil and Water Contaminants (Kruger, E., Anderson, T. and Coats, J., eds) Washington, D.C. : ACS Symposium Series 664, pp. 2-17. 12. Bañuelos, G. and Schrale, G. (1989) Plants that remove selenium from soils. Calif. Agric. 43, 19-20. 13. Bañuelos, G.S., Ajwa, H.A., Mackey, M., Wu, L., Cook, C., Akohoue, S. and Zambruzuski, S. (1997) Accumulation of selenium by different plant species grown under increasing sodium and calcium chloride salinity. J. Environ. Qual. 26, 639-646.



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Research Institute of Meijo University, Tenpaku-ku, Nagoya, 468-8502, Japan Faculty of Science and Technology, Meijo University, Tenpaku-ku, Nagoya, 4688502, Japan

Abstract. Drought and salinity are among the worst scourges of agriculture. One effective mechanism to reduce damage from these stresses is the accumulation of high intracellular levels of osmoprotectant compounds. Glycinebetaine is a typical osmoprotectant. Recent studies demonstrated that the introduction of betaine accumulation pathways improves the stress tolerance of plants. Metabolic engineering is a useful technique to improve stress tolerance of important crops. The levels of betaine accumulation is determined by the rates of betaine synthesis, betaine uptake and efllux, and metabolisms. Although betaine is synthesized from choline in plants, some halotolerant cyanobacterium synthesizes betaine from glycine by three step methylation. Introduction of betaine synthesis pathways into plants have been examined. It is largely unknown how betaine is transported among plants. Only few betaine transporter genes have been isolated. In addition to the stress tolerance of plants, betaine uptake from foods would play an important role in human nutrition. As a methyl donor, betaine participates in the methionine cycle. In this review, recent progress on metabolic engineering of betaine will be described.

1. INTRODUCTION Cells of many organisms experience a variety of environmental stresses such as high external osmolality, desiccation, and drought that reduce the amount of intracellular water [1-3]. In response to these water stresses, both prokaryotic and eukaryotic cells transport or synthesize highly soluble, low molecular weight compounds called osmolytes or osmoprotectants that allow the organism to take up and retain cellular water [4-6] and resume or sustain normal cellular processes. Osmolytes include Nmethylated amino acids and amines (glycine betaine, sarcosine, and trimethylamineN-oxide), amino acids (glycine, proline, and glutamate), and polyols (manitol and trehalose). Structures of some osmoprotectants are shown in Fig. 1. Glycine betaine (N,N,N-trimethylglycine, GB) is one of the most widespread osmolytes, found in bacteria, halophilic archaebacteria, marine invertebrates, plants, and mammalians [5,6]. Recent research on several aspects of betaine attracts considerable attentions. These are on biosynthetic pathway of betaine [7-9], new concept “osmophobic effects” [10], transport of betaine [11,12] genetic engineering 137 Ashwani K. Rai and Teruhiro Takabe (eds.), Abiotic Stress Tolerance in Plants, 137-151. © 2006 Springer. Printed in the Netherlands.



of betaine [13-16], and role of betaine on human health [17]. In this review, we discuss on these subjects. CH2 OH OH



glycine betaine

HO- C -H



H- C -OH







CH2 OH HO- C -H HO- C -H

H- C -OH

H- C -OH

H- C -OH

H- C -OH





Figure 1. Structures of some osmoprotectants.

2. PHYSIOLOGICAL ROLES OF GLYCINE BETAINE Betaine is found in microorganisms, plants, and animals [4-7] and is a significant component of many foods [17], including wheat, shellfish, spinach, and sugar beets. Betaine is a zwitterionic quaternary ammonium compound that is also known as trimethylglycine, glycine betaine, lycine, and oxyneurine. It is a methyl derivative of the amino acid glycine with a molecular weight of 117.2 and has been characterized as a methylamine because of its 3 chemically reactive methyl groups. Betaine was first discovered in the juice of sugar beets (Beta vulgaris) in the 19th century and was subsequently found in several other organisms. The physiologic function of betaine is either as an organic osmolyte to protect cells under stress or as a catabolic source of methyl groups via transmethylation for use in many biochemical pathways [17]. The principle role for betaine in plants and microorganisms is to protect cells against osmotic inactivation [4-6,18,19] Exposure to drought, high salinity, or temperature stress triggers betaine synthesis in chloroplast in plants [7,8], mitochondria in animal [20,21] or cytosol in bacteria [22], which results in its accumulation in the cells. Betaine is a compatible osmolyte that increases the water retention of cells, replaces inorganic salts, and protects intracellular enzymes against osmotically induced or temperature induced inactivation [23]. For example, spinach is grown in saline soil, and betaine can accumulate in amounts of up to 3% of fresh weight. This enables the chloroplasts to photosynthesize in the presence of high salinity [24]. 3. OSMOPHOBIC EFFECTS Protein stability plays an important role not only in its biological function but also in medical science and protein engineering. Osmolytes can protect proteins from the unfolding and aggregation induced by extreme environmental stress [10]. Significant progress on molecular mechanisms of osmolytes has been made recently [23,25]. It was found that the protective effects of osmolytes are a result of enhancing the



structural stability of native protein. The effects of osmolytes on preventing proteins against aggregation are due to the preferential increase of free energy of the activated complex (unfolded protein) which shifts the equilibrium between the native state and the activated complex to favor the native state (Fig. 2). The effect of osmolytes on the free energy of the native protein is small.

Free energy G

in osmolyte Unfolded protein in water Native protein in osmolyte in water

Figure 2. A schematic diagram of free energy in water and osmolyte.

The protection of enzyme activity by osmolytes is due to the enhancement of the structural stability of the whole protein rather than the active site. In natural selection of organic osmolytes as protein stabilizers, it appears that the osmolyte was selected as molecules which exhibit the unfavorable interaction with the peptide backbone (osmophobic effect) [10,23,25]. Because the peptide backbone is highly exposed to osmolyte in the denatured state, the osmophobic effect preferentially raises the free energy of the denatured state, shifting the equilibrium in favor of the native state. Since the osmophobic effect is the interaction on the denatured state, the native state is relatively unfettered by the presence of osmolyte. The osmophobic effect is a new thermodynamic force in nature that complements the well-recognized hydrophobic interactions, hydrogen bonding, electrostatic and dispersion forces that drive protein folding. Osmolytes are preferentially excluded from folded protein surface which is equivalent to preferential interaction with water rather than with the solute. As a result, the local concentration of the solute at the protein surface is less than its bulk concentration. Under high concentrations of osmolytes, the efficient osmophobic effects are anticipated which has been proposed to be the basis of their evolutionary selection [10,23,25] 4. BIOSYNTHETIC PATHWAYS OF GLYCINEBETAINE Most known biosynthetic pathways of betaine include a two-step oxidation of choline: choline → betaine aldehyde → betaine (Fig. 3). The first step is catalyzed by choline monooxygenase (CMO) in plants [8], choline dehydrogenase (CDH) in animals [20] and bacteria [18,22], and choline oxidase (COD) in some bacteria [26]. The second step is catalyzed by NAD+-dependent betaine aldehyde dehydrogenase (BADH) [7,18,21] in all organisms although in some bacteria, choline



dehydrogenase and choline oxidase also catalyze the second step. CDH is the membrane bound enzyme linked to respirately electron transport systems in E. coli and animals [18,20]. In mamalian, CDH [20] and BADH [21] are localized in mitochondria . COD is a soluble enzyme known in Arthrobacter globiformis. O2 2H2 O Fdred Fdox










CH3 betaine

betaine aldehyde












2O2 , H2 O 2H2 O2


CH3 betaine






betaine aldehyde







Figure 3. Betaine synthetic pathways from choline.

In plants, the first step is catalyzed by a novel Rieske-type iron-sulfur enzyme choline monooxygenase (CMO) which is not found in animals and bacteria [8]. CMO [8] and BADH [7] are localized in chloroplasts. CMO is not well known, having so far been found only in Chenopodiaceae (spinach and sugar beet) and Amaranthaceae [6-8], and not detected even in some betaine accumulating plants such as mangrove [27]. Betaine accumulating mangrove, Avicennia marina, contains two BADH genes, but CMO gene could not be detected [27]. CMO enzyme is soluble and insensitive to carbon monooxide, contains an Rieske-type iron-sulfur center, and consists of hom*o-dimer or -trimer of subunit Mr 42,000 [8]. These [2Fe-2S] center Cys181


Fe binding

Fe 3+ S S


Fe 2+

Fe 2+ His164





Figure 4. A schematic structure of active site of CMO.



properties are completely unrelated to CDH, COD, and cytochrome P-450 type monooxygenases. The importance of Cys181 and His287 for binding of Fe-S cluster and Fe was demonstrated (Fig. 4) [28]. Spinach BADH has very short or no transit peptide, suggesting the targetting signal in mature coding region. Barley has a salt inducible BADH localized in peroxisome [29]. It has a tri-peptide SKL at the Cterminus [29]. Betaine accumulating mangrove (Avicennia marina) and barley have at least two BADH genes [27,30]. One chloroplast and the other is peroxisome localized, BADHs, [27,30]. Since CMO gene could not be detected in both plants, physiological function of multiple BADHs and biosynthetic pathway of betaine are unknown. Although spinach BADH is dimers and E. coli BADH is tetramer, both BADHs catalyzed the oxidation of not only betaine aldehyde but also omega aldehyde [31]. The affinities for betaine aldehyde were similar in the spinach and E. coli BADHs, whereas those for omega-aminoaldehydes were higher in spinach BADH than in E. coli BADH [32]. In contrast, the mangrove (Avicennia marina) BADH efficiently catalyzed the oxidation of betainealdehyde, but not the oxidation of omega-aminoaldehydes and were more stable at high temperature than the spinach BADH [27]. Recently, it was shown that a halotolerant cyanobacterium Aphanothece halophytica isolated from Dead Sea, has a novel biosynthetic pathway of betaine from glycine [33]. Two N-methyltransferase genes were involved for it (Fig. 5). One of gene products (GSMT) catalyzed the methylation reactions of glycine and sarcosine with S-adenosylmethionine (AdoMet, SAM) acting as the methyl donor. The other one (DMT) specifically catalyzed the methylation of dimethylglycine to betaine. Both enzymes are active as monomers. Betaine, a final product, did not show the feed back inhibition for the methyltransferases even in the presence of 2 M. A reaction product, S-adenosyl hom*ocysteine (AdoHcy), inhibited the methylation reactions with relatively low affinities. The co-expressing of two enzymes in E. coli increased the betaine level and enhanced the growth rates. Immunoblot analysis revealed the increased accumulation of these enzymes in Aphanothece halophytica cells under high salinity. AdoMet









H sarcosine








CH3 betaine

Figure 5. Betaine synthesis pathway by glycine methylation.

5. GENETIC ENGINEERING OF GLYCINE BETAINE In the natural environment, plants often grow under unfavorable conditions, such as drought, salinity, chilling, high temperature, wounding, or strong light. These



conditions are known collectively as abiotic stresses which can delay growth and development, reduce productivity and, in extreme cases, cause the plant to die [1-3]. Glycine betaine is synthesized in some plant species at elevated rates in response to various types of environmental stress [5-8]. Whereas in many plants, such as Arabidopsis, rice (Oryza sativa), and tobacco (Nicotiana tabacum), betaine can not be detected or negligible level if any. Glycine betaine appears to be a critical determinant of stress tolerance. The concentrations of betaine is correlated with the level of tolerance. Moreover, exogenous application of glycine betaine improves the growth and survival of a wide variety of plants under various stresses. Transgenic plants of various species have been produced that express CMO, CDH, or COD [13-16,28,33]. For the expression of CMO and CDH, BADH gene was also expressed although betaine synthesis occurs via the use of BADH gene from host plants. These plants accumulate glycine betaine at various levels and exhibit enhanced tolerance of several types of stress. The metabolic engineering of glycine betaine thus appear to be an effective method for improving stress tolerance. However, the accumulation levels of glycine betaine in transgenic plants are generally low (

Abiotic Stress Tolerance in Plants: Toward the Improvement of Global Environment and Food - PDF Free Download (2024)


What is abiotic stress tolerance in plants? ›

Abiotic stress is the adverse effect of any abiotic factor on a plant in a given environment, impacting plants' growth and development. These stress factors, such as drought, salinity, and extreme temperatures, are often interrelated or in conjunction with each other.

Which abiotic stress can be tolerated by genetically modified crops? ›

In addition to that, the transgenic lines also expressed better tolerance to a variety of abiotic stresses including high temperature, drought, salinity and chilling stress.

What are the 2 main abiotic stresses that plants must adapt to? ›

Abiotic stress is defined as the negative impact of non-living factors on living organisms in a specific environment. The stresses include drought, salinity, low or high temperatures, and other environmental extremes. Abiotic stresses, especially hypersalinity and drought, are the primary causes of crop loss worldwide.

What are plant abiotic stress challenges from the changing environment? ›

The challenges of abiotic stress on plant growth and development are evident among the emerging ecological impacts of climate change (Bellard et al., 2012), and the constraints to crop production exacerbated with the increasing human population competing for environmental resources (Wallace et al., 2003).

How to overcome abiotic stress in plants? ›

They can prevent abiotic stress by: Improving rooting: When starting the cultivation of the plant, the plant's resistance should be taken into account as early as possible, a better rooted plant is more resistant to stress factors, such as drought or lack of nutrients, among others.

What is tolerance to abiotic environment? ›

Just as species have geographic ranges, they also have tolerance ranges for the abiotic environmental conditions. In other words, they can tolerate (or survive within) a certain range of a particular factor, but cannot survive if there is too much or too little of the factor. Take temperature, for example.

How are crops tolerant to abiotic stress? ›

Adoption and cultivation of varieties with tolerance to the deficit and excess moisture, heat, cold, and salinity in vulnerable agroecosystems play a crucial role. This relies on the development, popularization, and availability of abiotic stress-tolerant crop varieties (ASTCVs) to farming communities.

What are two examples of crops genetically modified for resistance to environmental stress? ›

Conventional breeding methods have a limited potential to improve plant genomes against environmental stress. Recently, genetic engineering has contributed enormously to the development of genetically modified varieties of different crops such as cotton, maize, rice, canola and soybean.

What are the effects of abiotic stresses on plant growth and development? ›

Abiotic stresses, such as low or high temperature, deficient or excessive water, high salinity, heavy metals, and ultraviolet radiation, are hostile to plant growth and development, leading to great crop yield penalty worldwide.

What is the conclusion of abiotic stress in plants? ›

Abiotic stress negatively influences plant survival and plant productivity. Usually, multiple genes are responsible for controlling stress resistance response; hence it limits the breeding applications to improve crops with abiotic stress tolerance.

What are plant defense mechanisms against abiotic stress? ›

Plants activate appropriate defense mechanisms, including induced systemic resistance and systemic acquired resistance, mediated by plant growth–promoting bacteria and fungi. Phytohormones such as ethylene, jasmonic acid, and salicylic acid play as key modulators in the induction of immune mechanisms in plants.

How do plants evolve to face abiotic stress? ›

Avoidance Strategies: Some plants have evolved avoidance strategies that allow them to sidestep the immediate impact of abiotic stress. For instance, they may exhibit early flowering to escape drought or produce waxy coatings to reduce water loss through transpiration.

What are the abiotic stress tolerance mechanisms in plants? ›

These mechanisms include stress perception, signal transduction, transcriptional activation of stress-responsive target genes, and synthesis of stress-related proteins and other molecules, which assist plants to cope with adverse environmental conditions through biochemical and physiological manifestations.

What are the symptoms of abiotic stress in plants? ›

Common symptoms of abiotic stresses may include the following:
  • Wilting from insufficient soil water, or incipient wilting due to rate of transpiration greater than the rate at which roots absorb water.
  • Defoliation and dieback due to chronic water deficit.

What are the abiotic factors that affect plant growth and development? ›

and abiotic factors (i.e., sunlight, temperature, rain, humidity, drought, salinity, air, soil, pollution, magnetic fields, etc.) can affect plant growth and crop yield in many different ways.

What is tolerance of abiotic factors? ›

The range between the upper and lower limits is known as tolerance range for the abiotic factor. Death occurs beyond this range. For example, for most animals the minimum temperature limit is 0oC and maximum limit of 42oC .

What are the abiotic factors of plant stress? ›

Different abiotic stresses, such as cold, heat, drought, flood, and salt can provoke common cellular disorder and secondary stresses, including membrane injury, reactive species (RS) damage, protein denaturation, and osmotic stress, which are also interconnected with each other.

What is a stress-tolerant plant? ›

Stress-tolerant plants establish a new metabolic homeostasis in response to stress and thereby can continue to grow without suffering stress-induced injury. Tolerance mechanisms are coordinated and fine-tuned by adjusting growth, development, and cellular and molecular activities (Levitt, 1980).

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